7-131682203-C-T

Variant names:

• chr7-131682203-C-T
• rs12536699

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.608

Alfa AF: 0.615 Hom.: 12269

Bravo AF: 0.615

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12536699; hg19: chr7-131366962;