rs10491857

Variant names:

• chr9-1512232-T-C
• rs10491857

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 0.125 in 152,030 control chromosomes in the GnomAD database, including 1,263 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 0.13 (1263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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: 0.125 AC: 19027 AN: 151912 Hom.: 1263 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0961

Gnomad SAS AF: 0.0440

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.125 AC: 19032 AN: 152030 Hom.: 1263 Cov.: 32 AF XY: 0.123 AC XY: 9151 AN XY: 74322

African (AFR) AF: 0.162 AC: 6717 AN: 41470

American (AMR) AF: 0.102 AC: 1566 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3470

East Asian (EAS) AF: 0.0964 AC: 497 AN: 5158

South Asian (SAS) AF: 0.0442 AC: 213 AN: 4814

European-Finnish (FIN) AF: 0.104 AC: 1101 AN: 10576

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

European-Non Finnish (NFE) AF: 0.115 AC: 7846 AN: 67954

Other (OTH) AF: 0.133 AC: 280 AN: 2108

Alfa AF: 0.117 Hom.: 1795

Bravo AF: 0.128

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.55
DANN	Benign	0.75
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10491857; hg19: chr9-1512232;