rs4938179

Variant names:

• chr11-115162705-G-T
• rs4938179

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 0.197 in 152,072 control chromosomes in the GnomAD database, including 3,634 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 0.20 (3634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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: 0.197 AC: 29970 AN: 151952 Hom.: 3629 Cov.: 32

Gnomad AFR AF: 0.0685

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.197 AC: 29978 AN: 152072 Hom.: 3634 Cov.: 32 AF XY: 0.201 AC XY: 14918 AN XY: 74320

African (AFR) AF: 0.0683 AC: 2833 AN: 41490

American (AMR) AF: 0.275 AC: 4197 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3468

East Asian (EAS) AF: 0.152 AC: 784 AN: 5154

South Asian (SAS) AF: 0.334 AC: 1606 AN: 4812

European-Finnish (FIN) AF: 0.273 AC: 2882 AN: 10564

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16550 AN: 67982

Other (OTH) AF: 0.195 AC: 412 AN: 2110

Alfa AF: 0.213 Hom.: 585

Bravo AF: 0.188

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.7
DANN	Benign	0.75
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs4938179; hg19: chr11-115033425;