rs10492294

Variant names:

• chr8-128234169-T-C
• rs10492294

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 0.171 in 152,178 control chromosomes in the GnomAD database, including 2,706 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 0.17 (2706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 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: 0.171 AC: 25956 AN: 152060 Hom.: 2702 Cov.: 32

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.171 AC: 25967 AN: 152178 Hom.: 2706 Cov.: 32 AF XY: 0.172 AC XY: 12773 AN XY: 74392

African (AFR) AF: 0.0491 AC: 2038 AN: 41548

American (AMR) AF: 0.212 AC: 3242 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1052 AN: 3470

East Asian (EAS) AF: 0.152 AC: 787 AN: 5180

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4824

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10588

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15084 AN: 67968

Other (OTH) AF: 0.186 AC: 392 AN: 2110

Alfa AF: 0.205 Hom.: 11430

Bravo AF: 0.165

Asia WGS AF: 0.187 AC: 650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.65
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs10492294; hg19: chr8-129246415;