rs10958409

Variant names:

• chr8-54414531-G-A
• rs10958409

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 0.181 in 152,132 control chromosomes in the GnomAD database, including 2,734 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 0.18 (2734 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 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: 0.181 AC: 27440 AN: 152014 Hom.: 2735 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.181 AC: 27460 AN: 152132 Hom.: 2734 Cov.: 33 AF XY: 0.186 AC XY: 13824 AN XY: 74378

African (AFR) AF: 0.165 AC: 6848 AN: 41500

American (AMR) AF: 0.259 AC: 3965 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1503 AN: 5162

South Asian (SAS) AF: 0.347 AC: 1676 AN: 4826

European-Finnish (FIN) AF: 0.195 AC: 2060 AN: 10560

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10464 AN: 68014

Other (OTH) AF: 0.172 AC: 362 AN: 2110

Alfa AF: 0.167 Hom.: 10405

Bravo AF: 0.184

Asia WGS AF: 0.295 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.67
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10958409; hg19: chr8-55327091;