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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 14-77278764-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=77278764&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 77278764,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_013382.7",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1997A>G",
"hgvs_p": "p.Tyr666Cys",
"transcript": "NM_013382.7",
"protein_id": "NP_037514.2",
"transcript_support_level": null,
"aa_start": 666,
"aa_end": null,
"aa_length": 750,
"cds_start": 1997,
"cds_end": null,
"cds_length": 2253,
"cdna_start": 2199,
"cdna_end": null,
"cdna_length": 4875,
"mane_select": "ENST00000261534.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_013382.7"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1997A>G",
"hgvs_p": "p.Tyr666Cys",
"transcript": "ENST00000261534.9",
"protein_id": "ENSP00000261534.4",
"transcript_support_level": 1,
"aa_start": 666,
"aa_end": null,
"aa_length": 750,
"cds_start": 1997,
"cds_end": null,
"cds_length": 2253,
"cdna_start": 2199,
"cdna_end": null,
"cdna_length": 4875,
"mane_select": "NM_013382.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261534.9"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.2144A>G",
"hgvs_p": "p.Tyr715Cys",
"transcript": "ENST00000682795.1",
"protein_id": "ENSP00000507574.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 799,
"cds_start": 2144,
"cds_end": null,
"cds_length": 2400,
"cdna_start": 2204,
"cdna_end": null,
"cdna_length": 2828,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682795.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.2081A>G",
"hgvs_p": "p.Tyr694Cys",
"transcript": "ENST00000923942.1",
"protein_id": "ENSP00000594001.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 778,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2337,
"cdna_start": 2273,
"cdna_end": null,
"cdna_length": 2914,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923942.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.2078A>G",
"hgvs_p": "p.Tyr693Cys",
"transcript": "ENST00000947742.1",
"protein_id": "ENSP00000617801.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 777,
"cds_start": 2078,
"cds_end": null,
"cds_length": 2334,
"cdna_start": 2268,
"cdna_end": null,
"cdna_length": 2909,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947742.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.2036A>G",
"hgvs_p": "p.Tyr679Cys",
"transcript": "ENST00000905355.1",
"protein_id": "ENSP00000575414.1",
"transcript_support_level": null,
"aa_start": 679,
"aa_end": null,
"aa_length": 763,
"cds_start": 2036,
"cds_end": null,
"cds_length": 2292,
"cdna_start": 2195,
"cdna_end": null,
"cdna_length": 4871,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905355.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1754A>G",
"hgvs_p": "p.Tyr585Cys",
"transcript": "ENST00000947744.1",
"protein_id": "ENSP00000617803.1",
"transcript_support_level": null,
"aa_start": 585,
"aa_end": null,
"aa_length": 669,
"cds_start": 1754,
"cds_end": null,
"cds_length": 2010,
"cdna_start": 1943,
"cdna_end": null,
"cdna_length": 2570,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947744.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1556A>G",
"hgvs_p": "p.Tyr519Cys",
"transcript": "ENST00000947743.1",
"protein_id": "ENSP00000617802.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 603,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 1723,
"cdna_end": null,
"cdna_length": 2372,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947743.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1538A>G",
"hgvs_p": "p.Tyr513Cys",
"transcript": "ENST00000556394.2",
"protein_id": "ENSP00000451967.2",
"transcript_support_level": 3,
"aa_start": 513,
"aa_end": null,
"aa_length": 597,
"cds_start": 1538,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1717,
"cdna_end": null,
"cdna_length": 4382,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000556394.2"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.2225A>G",
"hgvs_p": "p.Tyr742Cys",
"transcript": "XM_047431312.1",
"protein_id": "XP_047287268.1",
"transcript_support_level": null,
"aa_start": 742,
"aa_end": null,
"aa_length": 826,
"cds_start": 2225,
"cds_end": null,
"cds_length": 2481,
"cdna_start": 2427,
"cdna_end": null,
"cdna_length": 5103,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431312.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.2186A>G",
"hgvs_p": "p.Tyr729Cys",
"transcript": "XM_011536675.3",
"protein_id": "XP_011534977.1",
"transcript_support_level": null,
"aa_start": 729,
"aa_end": null,
"aa_length": 813,
"cds_start": 2186,
"cds_end": null,
"cds_length": 2442,
"cdna_start": 2388,
"cdna_end": null,
"cdna_length": 5064,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011536675.3"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.2036A>G",
"hgvs_p": "p.Tyr679Cys",
"transcript": "XM_047431313.1",
"protein_id": "XP_047287269.1",
"transcript_support_level": null,
"aa_start": 679,
"aa_end": null,
"aa_length": 763,
"cds_start": 2036,
"cds_end": null,
"cds_length": 2292,
"cdna_start": 2238,
"cdna_end": null,
"cdna_length": 4914,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431313.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1892A>G",
"hgvs_p": "p.Tyr631Cys",
"transcript": "XM_047431314.1",
"protein_id": "XP_047287270.1",
"transcript_support_level": null,
"aa_start": 631,
"aa_end": null,
"aa_length": 715,
"cds_start": 1892,
"cds_end": null,
"cds_length": 2148,
"cdna_start": 2342,
"cdna_end": null,
"cdna_length": 5018,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431314.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1766A>G",
"hgvs_p": "p.Tyr589Cys",
"transcript": "XM_047431316.1",
"protein_id": "XP_047287272.1",
"transcript_support_level": null,
"aa_start": 589,
"aa_end": null,
"aa_length": 673,
"cds_start": 1766,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 1968,
"cdna_end": null,
"cdna_length": 4644,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431316.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1727A>G",
"hgvs_p": "p.Tyr576Cys",
"transcript": "XM_011536677.4",
"protein_id": "XP_011534979.1",
"transcript_support_level": null,
"aa_start": 576,
"aa_end": null,
"aa_length": 660,
"cds_start": 1727,
"cds_end": null,
"cds_length": 1983,
"cdna_start": 1929,
"cdna_end": null,
"cdna_length": 4605,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011536677.4"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1628A>G",
"hgvs_p": "p.Tyr543Cys",
"transcript": "XM_047431317.1",
"protein_id": "XP_047287273.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 627,
"cds_start": 1628,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 1897,
"cdna_end": null,
"cdna_length": 4573,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431317.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1538A>G",
"hgvs_p": "p.Tyr513Cys",
"transcript": "XM_047431318.1",
"protein_id": "XP_047287274.1",
"transcript_support_level": null,
"aa_start": 513,
"aa_end": null,
"aa_length": 597,
"cds_start": 1538,
"cds_end": null,
"cds_length": 1794,
"cdna_start": 1740,
"cdna_end": null,
"cdna_length": 4416,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431318.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1280A>G",
"hgvs_p": "p.Tyr427Cys",
"transcript": "XM_047431319.1",
"protein_id": "XP_047287275.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 511,
"cds_start": 1280,
"cds_end": null,
"cds_length": 1536,
"cdna_start": 1589,
"cdna_end": null,
"cdna_length": 4265,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431319.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1091A>G",
"hgvs_p": "p.Tyr364Cys",
"transcript": "XM_047431320.1",
"protein_id": "XP_047287276.1",
"transcript_support_level": null,
"aa_start": 364,
"aa_end": null,
"aa_length": 448,
"cds_start": 1091,
"cds_end": null,
"cds_length": 1347,
"cdna_start": 1400,
"cdna_end": null,
"cdna_length": 4076,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431320.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1986A>G",
"hgvs_p": "p.Leu662Leu",
"transcript": "ENST00000682247.1",
"protein_id": "ENSP00000507213.1",
"transcript_support_level": null,
"aa_start": 662,
"aa_end": null,
"aa_length": 774,
"cds_start": 1986,
"cds_end": null,
"cds_length": 2325,
"cdna_start": 2107,
"cdna_end": null,
"cdna_length": 2729,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682247.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.*28A>G",
"hgvs_p": null,
"transcript": "XM_047431315.1",
"protein_id": "XP_047287271.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 685,
"cds_start": null,
"cds_end": null,
"cds_length": 2058,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2323,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431315.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"hgvs_c": "c.1892-256A>G",
"hgvs_p": null,
"transcript": "ENST00000682467.1",
"protein_id": "ENSP00000508062.1",
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{
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{
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],
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{
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"transcript": "ENST00000683828.1",
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000683828.1"
}
],
"gene_symbol": "POMT2",
"gene_hgnc_id": 19743,
"dbsnp": "rs200198778",
"frequency_reference_population": 0.00009420083,
"hom_count_reference_population": 0,
"allele_count_reference_population": 152,
"gnomad_exomes_af": 0.0000944151,
"gnomad_genomes_af": 0.0000921392,
"gnomad_exomes_ac": 138,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.980226993560791,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.979,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9308,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.61,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.895,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM1",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_013382.7",
"gene_symbol": "POMT2",
"hgnc_id": 19743,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1997A>G",
"hgvs_p": "p.Tyr666Cys"
}
],
"clinvar_disease": " type A2, type B2,Autosomal recessive limb-girdle muscular dystrophy type 2N,Muscular dystrophy,Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies),Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability),POMT2-related disorder,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8 LP:2",
"phenotype_combined": "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2|Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2|not provided|Muscular dystrophy|Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2;Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2;Autosomal recessive limb-girdle muscular dystrophy type 2N|POMT2-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}