7-131682203-C-T

Variant names:

• chr7-131682203-C-T
• rs12536699

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.613 in 152,074 control chromosomes in the GnomAD database, including 29,434 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (29434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93106 AN: 151956 Hom.: 29413 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.615

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.613 AC: 93173 AN: 152074 Hom.: 29434 Cov.: 32 AF XY: 0.606 AC XY: 45059 AN XY: 74332

African (AFR) AF: 0.650 AC: 26966 AN: 41460

American (AMR) AF: 0.608 AC: 9282 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1983 AN: 3472

East Asian (EAS) AF: 0.118 AC: 612 AN: 5184

South Asian (SAS) AF: 0.484 AC: 2331 AN: 4816

European-Finnish (FIN) AF: 0.593 AC: 6260 AN: 10560

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43532 AN: 67990

Other (OTH) AF: 0.608 AC: 1286 AN: 2116

Alfa AF: 0.617 Hom.: 13970

Bravo AF: 0.615

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0070
DANN	Benign	0.36
PhyloP100		-3.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12536699; hg19: chr7-131366962;