14-24361644-T-C

Variant names:

• chr14-24361644-T-C
• rs1950500

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 0.681 in 152,104 control chromosomes in the GnomAD database, including 35,437 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 0.68 (35437 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 66 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 (NFE) allele frequency at 95% confidence interval = 0.707 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: 0.681 AC: 103447 AN: 151986 Hom.: 35396 Cov.: 33

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.681 AC: 103550 AN: 152104 Hom.: 35437 Cov.: 33 AF XY: 0.683 AC XY: 50751 AN XY: 74348

African (AFR) AF: 0.629 AC: 26064 AN: 41468

American (AMR) AF: 0.611 AC: 9345 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2770 AN: 3468

East Asian (EAS) AF: 0.703 AC: 3639 AN: 5180

South Asian (SAS) AF: 0.695 AC: 3352 AN: 4826

European-Finnish (FIN) AF: 0.729 AC: 7715 AN: 10578

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48385 AN: 67974

Other (OTH) AF: 0.678 AC: 1435 AN: 2116

Alfa AF: 0.703 Hom.: 161906

Bravo AF: 0.665

Asia WGS AF: 0.719 AC: 2500 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	2.2
DANN	Benign	0.62
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1950500; hg19: chr14-24830850;