rs1957491

Variant names:

• chr14-43840512-T-A
• rs1957491

Your query was ambiguous. Multiple possible variants found:

• chr14-43840512-T-A
• chr14-43840512-T-G

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 0.531 in 151,662 control chromosomes in the GnomAD database, including 21,680 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 0.53 (21680 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.587 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: 0.531 AC: 80507 AN: 151542 Hom.: 21655 Cov.: 31

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.531 AC: 80579 AN: 151662 Hom.: 21680 Cov.: 31 AF XY: 0.524 AC XY: 38818 AN XY: 74110

African (AFR) AF: 0.578 AC: 23918 AN: 41408

American (AMR) AF: 0.597 AC: 9071 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2136 AN: 3462

East Asian (EAS) AF: 0.371 AC: 1900 AN: 5128

South Asian (SAS) AF: 0.460 AC: 2217 AN: 4816

European-Finnish (FIN) AF: 0.390 AC: 4111 AN: 10528

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35352 AN: 67822

Other (OTH) AF: 0.562 AC: 1183 AN: 2106

Alfa AF: 0.366 Hom.: 861

Bravo AF: 0.550

Asia WGS AF: 0.385 AC: 1333 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.53
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1957491; hg19: chr14-44309715;