rs2725653

Variant names:

• chr8-5731379-A-C
• rs2725653

Your query was ambiguous. Multiple possible variants found:

• chr8-5731379-A-C
• chr8-5731379-A-G

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 0.107 in 152,254 control chromosomes in the GnomAD database, including 1,069 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 0.11 (1069 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 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: 0.107 AC: 16280 AN: 152136 Hom.: 1061 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0927

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.107 AC: 16328 AN: 152254 Hom.: 1069 Cov.: 33 AF XY: 0.103 AC XY: 7662 AN XY: 74448

African (AFR) AF: 0.180 AC: 7490 AN: 41530

American (AMR) AF: 0.0767 AC: 1173 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4830

European-Finnish (FIN) AF: 0.0442 AC: 469 AN: 10606

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0927 AC: 6302 AN: 68004

Other (OTH) AF: 0.104 AC: 221 AN: 2116

Alfa AF: 0.0440 Hom.: 40

Bravo AF: 0.112

Asia WGS AF: 0.0240 AC: 84 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.61
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2725653; hg19: chr8-5588901;