rs10491858

Variant names:

• chr9-1510495-A-G
• rs10491858

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 0.113 in 152,176 control chromosomes in the GnomAD database, including 1,009 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 0.11 (1009 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17254 AN: 152058 Hom.: 1010 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0674

Gnomad SAS AF: 0.0427

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.113 AC: 17255 AN: 152176 Hom.: 1009 Cov.: 33 AF XY: 0.111 AC XY: 8284 AN XY: 74394

African (AFR) AF: 0.125 AC: 5188 AN: 41530

American (AMR) AF: 0.0988 AC: 1511 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3468

East Asian (EAS) AF: 0.0676 AC: 349 AN: 5166

South Asian (SAS) AF: 0.0430 AC: 207 AN: 4816

European-Finnish (FIN) AF: 0.104 AC: 1097 AN: 10594

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7832 AN: 67992

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.114 Hom.: 1944

Bravo AF: 0.114

Asia WGS AF: 0.0540 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.45
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs10491858; hg19: chr9-1510495; COSMIC: COSV55933288;