rs10096633

Variant names:

• chr8-19973410-C-T
• rs10096633

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 0.21 in 152,148 control chromosomes in the GnomAD database, including 4,753 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 0.21 (4753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 114 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 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: 0.209 AC: 31840 AN: 152030 Hom.: 4730 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.210 AC: 31901 AN: 152148 Hom.: 4753 Cov.: 32 AF XY: 0.205 AC XY: 15272 AN XY: 74404

African (AFR) AF: 0.425 AC: 17618 AN: 41450

American (AMR) AF: 0.140 AC: 2141 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3472

East Asian (EAS) AF: 0.108 AC: 559 AN: 5176

South Asian (SAS) AF: 0.110 AC: 533 AN: 4832

European-Finnish (FIN) AF: 0.102 AC: 1077 AN: 10604

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8639 AN: 68004

Other (OTH) AF: 0.186 AC: 393 AN: 2110

Alfa AF: 0.152 Hom.: 8114

Bravo AF: 0.223

Asia WGS AF: 0.133 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.67
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10096633; hg19: chr8-19830921;