rs7862611

chr9-25359871-C-T

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 0.26 in 151,742 control chromosomes in the GnomAD database, including 5,879 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 0.26 (5879 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39458 AN: 151624 Hom.: 5869 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.260 AC: 39498 AN: 151742 Hom.: 5879 Cov.: 32 AF XY: 0.262 AC XY: 19457 AN XY: 74138

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.248

Alfa AF: 0.195 Hom.: 6140

Bravo AF: 0.265

Asia WGS AF: 0.257 AC: 893 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7862611; hg19: chr9-25359869;