rs11621961

Variant names:

• chr14-94303139-C-T
• rs11621961

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 0.313 in 151,984 control chromosomes in the GnomAD database, including 8,058 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 0.31 (8058 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 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: 0.313 AC: 47566 AN: 151866 Hom.: 8045 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.313 AC: 47612 AN: 151984 Hom.: 8058 Cov.: 31 AF XY: 0.315 AC XY: 23364 AN XY: 74256

African (AFR) AF: 0.192 AC: 7982 AN: 41490

American (AMR) AF: 0.411 AC: 6278 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1129 AN: 5156

South Asian (SAS) AF: 0.281 AC: 1351 AN: 4808

European-Finnish (FIN) AF: 0.341 AC: 3595 AN: 10544

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25284 AN: 67946

Other (OTH) AF: 0.333 AC: 703 AN: 2108

Alfa AF: 0.347 Hom.: 41280

Bravo AF: 0.310

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.59
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11621961; hg19: chr14-94769476;