rs11921014

Variant names:

• chr3-141657298-C-A
• rs11921014

Your query was ambiguous. Multiple possible variants found:

• chr3-141657298-C-A
• chr3-141657298-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0297 in 152,306 control chromosomes in the GnomAD database, including 93 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 0.030 (93 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0297 (4520/152306) while in subpopulation NFE AF = 0.0435 (2957/68016). AF 95% confidence interval is 0.0422. There are 93 homozygotes in GnomAd4. There are 2134 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 93 gene

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: 0.0297 AC: 4520 AN: 152188 Hom.: 93 Cov.: 33

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0297 AC: 4520 AN: 152306 Hom.: 93 Cov.: 33 AF XY: 0.0287 AC XY: 2134 AN XY: 74470

African (AFR) AF: 0.0120 AC: 500 AN: 41568

American (AMR) AF: 0.0318 AC: 487 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0409 AC: 142 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4832

European-Finnish (FIN) AF: 0.0199 AC: 211 AN: 10616

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2957 AN: 68016

Other (OTH) AF: 0.0336 AC: 71 AN: 2112

Alfa AF: 0.0398 Hom.: 58

Bravo AF: 0.0306

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.96
DANN	Benign	0.27
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs11921014; hg19: chr3-141376140;