14-62656289-T-C

Variant names:

• chr14-62656289-T-C
• rs1953248

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 0.901 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.842 AC: 34993 AN: 41542

American (AMR) AF: 0.942 AC: 14401 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3200 AN: 3472

East Asian (EAS) AF: 0.733 AC: 3791 AN: 5170

South Asian (SAS) AF: 0.926 AC: 4472 AN: 4830

European-Finnish (FIN) AF: 0.909 AC: 9642 AN: 10604

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63651 AN: 68018

Other (OTH) AF: 0.897 AC: 1897 AN: 2116

Alfa AF: 0.920 Hom.: 125907

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
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs1953248; hg19: chr14-63123007;