rs944052

Variant names:

• chr14-64339114-G-A
• rs944052

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 0.181 in 152,132 control chromosomes in the GnomAD database, including 2,919 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 0.18 (2919 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 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: 0.181 AC: 27523 AN: 152014 Hom.: 2907 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.181 AC: 27580 AN: 152132 Hom.: 2919 Cov.: 32 AF XY: 0.181 AC XY: 13490 AN XY: 74352

African (AFR) AF: 0.261 AC: 10843 AN: 41506

American (AMR) AF: 0.135 AC: 2058 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 387 AN: 3472

East Asian (EAS) AF: 0.377 AC: 1939 AN: 5140

South Asian (SAS) AF: 0.0946 AC: 456 AN: 4822

European-Finnish (FIN) AF: 0.190 AC: 2015 AN: 10596

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9407 AN: 67990

Other (OTH) AF: 0.157 AC: 333 AN: 2116

Alfa AF: 0.167 Hom.: 401

Bravo AF: 0.184

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.62
DANN	Benign	0.72
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs944052; hg19: chr14-64805832;