7-81425636-T-C

Variant names:

• chr7-81425636-T-C
• rs2040902

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 0.529 in 151,862 control chromosomes in the GnomAD database, including 22,303 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 0.53 (22303 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 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: 0.529 AC: 80224 AN: 151744 Hom.: 22272 Cov.: 31

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.529 AC: 80316 AN: 151862 Hom.: 22303 Cov.: 31 AF XY: 0.526 AC XY: 39065 AN XY: 74222

African (AFR) AF: 0.654 AC: 27096 AN: 41440

American (AMR) AF: 0.649 AC: 9868 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3292 AN: 5146

South Asian (SAS) AF: 0.552 AC: 2659 AN: 4820

European-Finnish (FIN) AF: 0.330 AC: 3489 AN: 10572

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30530 AN: 67904

Other (OTH) AF: 0.539 AC: 1137 AN: 2110

Alfa AF: 0.486 Hom.: 2291

Bravo AF: 0.559

Asia WGS AF: 0.615 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs2040902; hg19: chr7-81054952; COSMIC: COSV107155130;