rs4665639

Variant names:

• chr2-20964019-A-G
• rs4665639

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 0.54 in 152,122 control chromosomes in the GnomAD database, including 22,754 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 0.54 (22754 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 4 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 = 0.838 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: 0.540 AC: 82081 AN: 152004 Hom.: 22757 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.540 AC: 82100 AN: 152122 Hom.: 22754 Cov.: 33 AF XY: 0.541 AC XY: 40247 AN XY: 74346

African (AFR) AF: 0.447 AC: 18542 AN: 41484

American (AMR) AF: 0.487 AC: 7451 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2316 AN: 3468

East Asian (EAS) AF: 0.859 AC: 4448 AN: 5178

South Asian (SAS) AF: 0.727 AC: 3509 AN: 4826

European-Finnish (FIN) AF: 0.520 AC: 5500 AN: 10574

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38424 AN: 67986

Other (OTH) AF: 0.561 AC: 1185 AN: 2114

Alfa AF: 0.560 Hom.: 40055

Bravo AF: 0.531

Asia WGS AF: 0.749 AC: 2602 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	5.0
DANN	Benign	0.55
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4665639; hg19: chr2-21186891;