10-33858367-T-C

Variant names:

• chr10-33858367-T-C
• rs10508791

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 0.132 in 152,248 control chromosomes in the GnomAD database, including 1,435 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 (1435 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 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: 0.132 AC: 20011 AN: 152130 Hom.: 1432 Cov.: 33

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0368

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.132 AC: 20023 AN: 152248 Hom.: 1435 Cov.: 33 AF XY: 0.131 AC XY: 9748 AN XY: 74426

African (AFR) AF: 0.0991 AC: 4119 AN: 41548

American (AMR) AF: 0.183 AC: 2805 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.0369 AC: 191 AN: 5182

South Asian (SAS) AF: 0.137 AC: 660 AN: 4826

European-Finnish (FIN) AF: 0.151 AC: 1597 AN: 10600

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

European-Non Finnish (NFE) AF: 0.142 AC: 9634 AN: 68016

Other (OTH) AF: 0.139 AC: 294 AN: 2112

Alfa AF: 0.139 Hom.: 2453

Bravo AF: 0.133

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.80
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10508791; hg19: chr10-34147295;