rs2569163

Variant names:

• chr5-140595881-A-G
• rs2569163

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 0.586 in 152,052 control chromosomes in the GnomAD database, including 26,899 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 0.59 (26899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 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: 0.586 AC: 88999 AN: 151934 Hom.: 26852 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.586 AC: 89108 AN: 152052 Hom.: 26899 Cov.: 32 AF XY: 0.589 AC XY: 43758 AN XY: 74338

African (AFR) AF: 0.719 AC: 29805 AN: 41482

American (AMR) AF: 0.535 AC: 8181 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1861 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2223 AN: 5174

South Asian (SAS) AF: 0.493 AC: 2377 AN: 4822

European-Finnish (FIN) AF: 0.646 AC: 6828 AN: 10566

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36295 AN: 67948

Other (OTH) AF: 0.557 AC: 1171 AN: 2102

Alfa AF: 0.557 Hom.: 9208

Bravo AF: 0.578

Asia WGS AF: 0.520 AC: 1809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.3
DANN	Benign	0.80
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2569163; hg19: chr5-139975466; COSMIC: COSV72544927;