rs1957491

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.562

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1957491; hg19: chr14-44309715;