rs1957860

Variant names:

• chr14-53962637-C-T
• rs1957860

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 0.518 in 152,024 control chromosomes in the GnomAD database, including 20,955 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 0.52 (20955 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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: 0.518 AC: 78680 AN: 151906 Hom.: 20932 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.518 AC: 78748 AN: 152024 Hom.: 20955 Cov.: 32 AF XY: 0.522 AC XY: 38805 AN XY: 74288

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.551

Alfa AF: 0.495 Hom.: 27653

Bravo AF: 0.532

Asia WGS AF: 0.709 AC: 2463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1957860; hg19: chr14-54429355;