rs2569163

Variant names:

• chr5-140595881-A-G
• rs2569163

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.557

Alfa AF: 0.561 Hom.: 5322

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

Splicing

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

Publications

LitVar

Other links and lift over

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