14-53962637-C-T

Variant names:

• chr14-53962637-C-T
• rs1957860

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 0.518 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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.524 AC: 21741 AN: 41454

American (AMR) AF: 0.614 AC: 9376 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1951 AN: 3472

East Asian (EAS) AF: 0.865 AC: 4468 AN: 5164

South Asian (SAS) AF: 0.559 AC: 2692 AN: 4812

European-Finnish (FIN) AF: 0.432 AC: 4560 AN: 10562

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32389 AN: 67970

Other (OTH) AF: 0.551 AC: 1161 AN: 2106

Alfa AF: 0.500 Hom.: 68114

Bravo AF: 0.532

Asia WGS AF: 0.709 AC: 2463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.39
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1957860; hg19: chr14-54429355;