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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: 11-3811305-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=3811305&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 3811305,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000278243.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_014489.4",
"protein_id": "NP_055304.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 315,
"cds_start": 46,
"cds_end": null,
"cds_length": 948,
"cdna_start": 148,
"cdna_end": null,
"cdna_length": 1963,
"mane_select": "ENST00000278243.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "ENST00000278243.9",
"protein_id": "ENSP00000278243.4",
"transcript_support_level": 1,
"aa_start": 16,
"aa_end": null,
"aa_length": 315,
"cds_start": 46,
"cds_end": null,
"cds_length": 948,
"cdna_start": 148,
"cdna_end": null,
"cdna_length": 1963,
"mane_select": "NM_014489.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.217C>T",
"hgvs_p": "p.Arg73Trp",
"transcript": "ENST00000300730.10",
"protein_id": "ENSP00000300730.6",
"transcript_support_level": 1,
"aa_start": 73,
"aa_end": null,
"aa_length": 307,
"cds_start": 217,
"cds_end": null,
"cds_length": 924,
"cdna_start": 242,
"cdna_end": null,
"cdna_length": 1843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "n.46C>T",
"hgvs_p": null,
"transcript": "ENST00000528216.5",
"protein_id": "ENSP00000432215.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.-304+2990C>T",
"hgvs_p": null,
"transcript": "ENST00000396993.8",
"protein_id": "ENSP00000380190.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 98,
"cds_start": -4,
"cds_end": null,
"cds_length": 297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "n.97+2990C>T",
"hgvs_p": null,
"transcript": "ENST00000465237.6",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.-158C>T",
"hgvs_p": null,
"transcript": "NM_001346399.2",
"protein_id": "NP_001333328.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 211,
"cds_start": -4,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.-158C>T",
"hgvs_p": null,
"transcript": "NM_001346401.2",
"protein_id": "NP_001333330.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 207,
"cds_start": -4,
"cds_end": null,
"cds_length": 624,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001256236.2",
"protein_id": "NP_001243165.2",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 315,
"cds_start": 46,
"cds_end": null,
"cds_length": 948,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 1978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "ENST00000464906.6",
"protein_id": "ENSP00000434631.2",
"transcript_support_level": 2,
"aa_start": 16,
"aa_end": null,
"aa_length": 315,
"cds_start": 46,
"cds_end": null,
"cds_length": 948,
"cdna_start": 135,
"cdna_end": null,
"cdna_length": 1259,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.217C>T",
"hgvs_p": "p.Arg73Trp",
"transcript": "ENST00000396986.6",
"protein_id": "ENSP00000380183.2",
"transcript_support_level": 2,
"aa_start": 73,
"aa_end": null,
"aa_length": 311,
"cds_start": 217,
"cds_end": null,
"cds_length": 936,
"cdna_start": 242,
"cdna_end": null,
"cdna_length": 1837,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.199C>T",
"hgvs_p": "p.Arg67Trp",
"transcript": "NM_001346397.2",
"protein_id": "NP_001333326.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 305,
"cds_start": 199,
"cds_end": null,
"cds_length": 918,
"cdna_start": 281,
"cdna_end": null,
"cdna_length": 1913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001346403.1",
"protein_id": "NP_001333332.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 295,
"cds_start": 46,
"cds_end": null,
"cds_length": 888,
"cdna_start": 156,
"cdna_end": null,
"cdna_length": 2050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001256240.2",
"protein_id": "NP_001243169.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 254,
"cds_start": 46,
"cds_end": null,
"cds_length": 765,
"cdna_start": 148,
"cdna_end": null,
"cdna_length": 1780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001283038.2",
"protein_id": "NP_001269967.2",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 254,
"cds_start": 46,
"cds_end": null,
"cds_length": 765,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 1795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001346398.2",
"protein_id": "NP_001333327.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 254,
"cds_start": 46,
"cds_end": null,
"cds_length": 765,
"cdna_start": 159,
"cdna_end": null,
"cdna_length": 1791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001346405.1",
"protein_id": "NP_001333334.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 254,
"cds_start": 46,
"cds_end": null,
"cds_length": 765,
"cdna_start": 156,
"cdna_end": null,
"cdna_length": 1788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "ENST00000463452.6",
"protein_id": "ENSP00000435223.1",
"transcript_support_level": 2,
"aa_start": 16,
"aa_end": null,
"aa_length": 254,
"cds_start": 46,
"cds_end": null,
"cds_length": 765,
"cdna_start": 129,
"cdna_end": null,
"cdna_length": 931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001145438.3",
"protein_id": "NP_001138910.2",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 250,
"cds_start": 46,
"cds_end": null,
"cds_length": 753,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 1783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001256239.2",
"protein_id": "NP_001243168.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 250,
"cds_start": 46,
"cds_end": null,
"cds_length": 753,
"cdna_start": 148,
"cdna_end": null,
"cdna_length": 1768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001346400.2",
"protein_id": "NP_001333329.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 250,
"cds_start": 46,
"cds_end": null,
"cds_length": 753,
"cdna_start": 159,
"cdna_end": null,
"cdna_length": 1779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "ENST00000469307.4",
"protein_id": "ENSP00000434507.1",
"transcript_support_level": 3,
"aa_start": 16,
"aa_end": null,
"aa_length": 244,
"cds_start": 46,
"cds_end": null,
"cds_length": 735,
"cdna_start": 109,
"cdna_end": null,
"cdna_length": 798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp",
"transcript": "NM_001256237.2",
"protein_id": "NP_001243166.2",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 234,
"cds_start": 46,
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},
{
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],
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},
{
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],
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},
{
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],
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"gene_symbol": "PGAP2",
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"transcript": "XM_047426792.1",
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"biotype": null,
"feature": null
}
],
"gene_symbol": "PGAP2",
"gene_hgnc_id": 17893,
"dbsnp": "rs773359554",
"frequency_reference_population": 0.000030360898,
"hom_count_reference_population": 0,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000314692,
"gnomad_genomes_af": 0.0000197148,
"gnomad_exomes_ac": 46,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4946593642234802,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.351,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3702,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.483,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000278243.9",
"gene_symbol": "PGAP2",
"hgnc_id": 17893,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.46C>T",
"hgvs_p": "p.Arg16Trp"
},
{
"score": 3,
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"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007062559.1",
"gene_symbol": "LOC124902618",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.412G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Hyperphosphatasia with intellectual disability syndrome 3",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Hyperphosphatasia with intellectual disability syndrome 3",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}