rs1957538

Variant names:

• chr14-81638187-G-C
• rs1957538

Your query was ambiguous. Multiple possible variants found:

• chr14-81638187-G-C
• chr14-81638187-G-T

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 0.558 in 152,120 control chromosomes in the GnomAD database, including 23,629 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 0.56 (23629 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84737 AN: 152002 Hom.: 23598 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.558 AC: 84820 AN: 152120 Hom.: 23629 Cov.: 33 AF XY: 0.562 AC XY: 41798 AN XY: 74358

African (AFR) AF: 0.541 AC: 22434 AN: 41486

American (AMR) AF: 0.640 AC: 9784 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1873 AN: 3470

East Asian (EAS) AF: 0.439 AC: 2269 AN: 5170

South Asian (SAS) AF: 0.614 AC: 2966 AN: 4828

European-Finnish (FIN) AF: 0.574 AC: 6075 AN: 10582

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37429 AN: 67980

Other (OTH) AF: 0.569 AC: 1200 AN: 2110

Alfa AF: 0.414 Hom.: 1044

Bravo AF: 0.561

Asia WGS AF: 0.587 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1957538; hg19: chr14-82104531;