rs4938025

Variant names:

• chr11-113512560-T-C
• rs4938025

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 0.261 in 152,146 control chromosomes in the GnomAD database, including 6,403 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 0.26 (6403 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 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: 0.261 AC: 39718 AN: 152026 Hom.: 6408 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.261 AC: 39716 AN: 152146 Hom.: 6403 Cov.: 32 AF XY: 0.270 AC XY: 20056 AN XY: 74356

African (AFR) AF: 0.0746 AC: 3099 AN: 41536

American (AMR) AF: 0.220 AC: 3363 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1004 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1647 AN: 5174

South Asian (SAS) AF: 0.378 AC: 1818 AN: 4810

European-Finnish (FIN) AF: 0.450 AC: 4754 AN: 10568

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

European-Non Finnish (NFE) AF: 0.341 AC: 23164 AN: 67984

Other (OTH) AF: 0.255 AC: 538 AN: 2112

Alfa AF: 0.311 Hom.: 6310

Bravo AF: 0.231

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.15
DANN	Benign	0.48
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4938025; hg19: chr11-113383282;