4-131377084-T-C

Variant names:

• chr4-131377084-T-C
• rs1911877

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 0.341 in 152,036 control chromosomes in the GnomAD database, including 9,006 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 0.34 (9006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.341 AC: 51833 AN: 151918 Hom.: 8993 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.341 AC: 51893 AN: 152036 Hom.: 9006 Cov.: 32 AF XY: 0.338 AC XY: 25119 AN XY: 74316

African (AFR) AF: 0.386 AC: 15985 AN: 41438

American (AMR) AF: 0.360 AC: 5489 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1164 AN: 3472

East Asian (EAS) AF: 0.190 AC: 985 AN: 5180

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4818

European-Finnish (FIN) AF: 0.290 AC: 3065 AN: 10580

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22586 AN: 67966

Other (OTH) AF: 0.363 AC: 766 AN: 2108

Alfa AF: 0.339 Hom.: 16655

Bravo AF: 0.351

Asia WGS AF: 0.300 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1911877; hg19: chr4-132298239;