rs10280709

Variant names:

• chr7-117973055-C-T
• rs10280709

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 0.328 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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

African (AFR) AF: 0.140 AC: 5803 AN: 41464

American (AMR) AF: 0.285 AC: 4351 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3470

East Asian (EAS) AF: 0.109 AC: 565 AN: 5162

South Asian (SAS) AF: 0.413 AC: 1988 AN: 4808

European-Finnish (FIN) AF: 0.549 AC: 5796 AN: 10562

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29041 AN: 67944

Other (OTH) AF: 0.314 AC: 661 AN: 2108

Alfa AF: 0.391 Hom.: 8783

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10280709; hg19: chr7-117613109;