rs1953248

Variant names:

• chr14-62656289-T-C
• rs1953248

Your query was ambiguous. Multiple possible variants found:

• chr14-62656289-T-C
• chr14-62656289-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 0.901 in 152,250 control chromosomes in the GnomAD database, including 61,995 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 0.90 (61995 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.93 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: 0.901 AC: 137042 AN: 152130 Hom.: 61940 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.901 AC: 137155 AN: 152250 Hom.: 61995 Cov.: 32 AF XY: 0.901 AC XY: 67065 AN XY: 74434

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.942

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.897

Alfa AF: 0.926 Hom.: 37173

Bravo AF: 0.898

Asia WGS AF: 0.872 AC: 3033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1953248; hg19: chr14-63123007;