rs10280709

Variant names:

• chr7-117973055-C-T
• rs10280709

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 0.328 in 151,990 control chromosomes in the GnomAD database, including 9,748 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 0.33 (9748 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 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: 0.328 AC: 49784 AN: 151872 Hom.: 9756 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.328 AC: 49777 AN: 151990 Hom.: 9748 Cov.: 31 AF XY: 0.335 AC XY: 24868 AN XY: 74296

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.314

Alfa AF: 0.408 Hom.: 6482

Bravo AF: 0.294

Asia WGS AF: 0.294 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10280709; hg19: chr7-117613109;