rs10491858

chr9-1510495-A-G

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 0.113 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.113 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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0988

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0676

Gnomad4 SAS AF: 0.0430

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.122

Alfa AF: 0.115 Hom.: 1441

Bravo AF: 0.114

Asia WGS AF: 0.0540 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.7
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

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