rs1953248

chr14-62656289-T-Cchr14-62656289-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;