rs4930431

Variant names:

• chr11-67526837-C-T
• rs4930431

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 0.371 in 152,116 control chromosomes in the GnomAD database, including 11,291 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 0.37 (11291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 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: 0.371 AC: 56438 AN: 151998 Hom.: 11289 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.371 AC: 56448 AN: 152116 Hom.: 11291 Cov.: 32 AF XY: 0.363 AC XY: 26968 AN XY: 74352

African (AFR) AF: 0.262 AC: 10852 AN: 41496

American (AMR) AF: 0.458 AC: 7013 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1030 AN: 3458

East Asian (EAS) AF: 0.167 AC: 866 AN: 5174

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4822

European-Finnish (FIN) AF: 0.333 AC: 3526 AN: 10578

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30668 AN: 67976

Other (OTH) AF: 0.368 AC: 777 AN: 2114

Alfa AF: 0.422 Hom.: 7769

Bravo AF: 0.381

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.78
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs4930431; hg19: chr11-67294308;