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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.557 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

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.569

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1957538; hg19: chr14-82104531;