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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: 2-227059468-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227059468&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 227059468,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000396625.5",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "NM_000092.5",
"protein_id": "NP_000083.3",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1690,
"cds_start": 2320,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 2620,
"cdna_end": null,
"cdna_length": 9984,
"mane_select": "ENST00000396625.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "ENST00000396625.5",
"protein_id": "ENSP00000379866.3",
"transcript_support_level": 5,
"aa_start": 774,
"aa_end": null,
"aa_length": 1690,
"cds_start": 2320,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 2620,
"cdna_end": null,
"cdna_length": 9984,
"mane_select": "NM_000092.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_005246281.4",
"protein_id": "XP_005246338.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1690,
"cds_start": 2320,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 2514,
"cdna_end": null,
"cdna_length": 9878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_047443228.1",
"protein_id": "XP_047299184.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1690,
"cds_start": 2320,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 2497,
"cdna_end": null,
"cdna_length": 9861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_011510557.3",
"protein_id": "XP_011508859.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1663,
"cds_start": 2320,
"cds_end": null,
"cds_length": 4992,
"cdna_start": 2620,
"cdna_end": null,
"cdna_length": 9903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2212G>A",
"hgvs_p": "p.Gly738Ser",
"transcript": "XM_011510558.3",
"protein_id": "XP_011508860.1",
"transcript_support_level": null,
"aa_start": 738,
"aa_end": null,
"aa_length": 1654,
"cds_start": 2212,
"cds_end": null,
"cds_length": 4965,
"cdna_start": 2512,
"cdna_end": null,
"cdna_length": 9876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_017003297.2",
"protein_id": "XP_016858786.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1651,
"cds_start": 2320,
"cds_end": null,
"cds_length": 4956,
"cdna_start": 2620,
"cdna_end": null,
"cdna_length": 9867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_006712246.4",
"protein_id": "XP_006712309.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1627,
"cds_start": 2320,
"cds_end": null,
"cds_length": 4884,
"cdna_start": 2620,
"cdna_end": null,
"cdna_length": 9795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_011510559.3",
"protein_id": "XP_011508861.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1612,
"cds_start": 2320,
"cds_end": null,
"cds_length": 4839,
"cdna_start": 2620,
"cdna_end": null,
"cdna_length": 6050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_011510560.3",
"protein_id": "XP_011508862.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1612,
"cds_start": 2320,
"cds_end": null,
"cds_length": 4839,
"cdna_start": 2620,
"cdna_end": null,
"cdna_length": 6027,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_047443241.1",
"protein_id": "XP_047299197.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1612,
"cds_start": 2320,
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"cdna_start": 2620,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
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"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_047443242.1",
"protein_id": "XP_047299198.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1612,
"cds_start": 2320,
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"cdna_start": 2620,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_011510561.3",
"protein_id": "XP_011508863.1",
"transcript_support_level": null,
"aa_start": 774,
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"aa_length": 1608,
"cds_start": 2320,
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"cdna_start": 2620,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 28,
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"exon_count": 49,
"intron_rank": null,
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"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_011510562.3",
"protein_id": "XP_011508864.1",
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_047443245.1",
"protein_id": "XP_047299201.1",
"transcript_support_level": null,
"aa_start": 774,
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"aa_length": 1608,
"cds_start": 2320,
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"cdna_start": 2620,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
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"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.1765G>A",
"hgvs_p": "p.Gly589Ser",
"transcript": "XM_005246282.4",
"protein_id": "XP_005246339.1",
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"mane_select": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_047443246.1",
"protein_id": "XP_047299202.1",
"transcript_support_level": null,
"aa_start": 774,
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"mane_select": null,
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_011510565.3",
"protein_id": "XP_011508867.1",
"transcript_support_level": null,
"aa_start": 774,
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"aa_length": 1424,
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},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 28,
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"intron_rank": null,
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"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_011510566.3",
"protein_id": "XP_011508868.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 28,
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"intron_rank": null,
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"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_011510567.3",
"protein_id": "XP_011508869.1",
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},
{
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"protein_coding": true,
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"consequences": [
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],
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"intron_rank": null,
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"gene_symbol": "COL4A4",
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"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_047443248.1",
"protein_id": "XP_047299204.1",
"transcript_support_level": null,
"aa_start": 774,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "G",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser",
"transcript": "XM_047443249.1",
"protein_id": "XP_047299205.1",
"transcript_support_level": null,
"aa_start": 774,
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"aa_length": 1420,
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"cdna_start": 2620,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "G",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
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"exon_count": 46,
"intron_rank": null,
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},
{
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}
],
"gene_symbol": "COL4A4",
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"dbsnp": "rs569681869",
"frequency_reference_population": 6.8404694e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84047e-7,
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"gnomad_exomes_ac": 1,
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"gnomad_exomes_homalt": 0,
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"computational_score_selected": 0.9948915839195251,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.959,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.483,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.53,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.101,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.07,
"spliceai_max_prediction": "Benign",
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"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000396625.5",
"gene_symbol": "COL4A4",
"hgnc_id": 2206,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.2320G>A",
"hgvs_p": "p.Gly774Ser"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}