rs2725369

Variant names:

• chr8-30993508-G-C
• rs2725369

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 0.683 in 152,000 control chromosomes in the GnomAD database, including 36,254 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 0.68 (36254 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 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: 0.683 AC: 103683 AN: 151882 Hom.: 36222 Cov.: 31

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.683 AC: 103773 AN: 152000 Hom.: 36254 Cov.: 31 AF XY: 0.684 AC XY: 50831 AN XY: 74304

African (AFR) AF: 0.810 AC: 33630 AN: 41494

American (AMR) AF: 0.713 AC: 10902 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 1999 AN: 3466

East Asian (EAS) AF: 0.959 AC: 4972 AN: 5186

South Asian (SAS) AF: 0.527 AC: 2529 AN: 4802

European-Finnish (FIN) AF: 0.653 AC: 6861 AN: 10508

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40834 AN: 67942

Other (OTH) AF: 0.651 AC: 1374 AN: 2110

Alfa AF: 0.634 Hom.: 3871

Bravo AF: 0.697

Asia WGS AF: 0.752 AC: 2608 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.67
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2725369; hg19: chr8-30851024;