rs2725369

Positions:

• chr8-30993508-G-C

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 0.683 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.651

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2725369; hg19: chr8-30851024;