7-132041373-T-C

Variant names:

• chr7-132041373-T-C
• rs4731839

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 0.123 in 152,208 control chromosomes in the GnomAD database, including 1,327 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 0.12 (1327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18779 AN: 152090 Hom.: 1328 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.123 AC: 18797 AN: 152208 Hom.: 1327 Cov.: 32 AF XY: 0.121 AC XY: 9026 AN XY: 74426

African (AFR) AF: 0.191 AC: 7908 AN: 41494

American (AMR) AF: 0.0857 AC: 1310 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3472

East Asian (EAS) AF: 0.162 AC: 838 AN: 5180

South Asian (SAS) AF: 0.0743 AC: 359 AN: 4830

European-Finnish (FIN) AF: 0.0926 AC: 982 AN: 10610

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0940 AC: 6395 AN: 68014

Other (OTH) AF: 0.130 AC: 273 AN: 2108

Alfa AF: 0.0973 Hom.: 1579

Bravo AF: 0.126

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.55
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs4731839; hg19: chr7-131726132;