rs10819634

Variant names:

• chr9-99097794-C-T
• rs10819634

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 0.223 in 152,130 control chromosomes in the GnomAD database, including 4,063 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 0.22 (4063 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 14 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 (EAS) allele frequency at 95% confidence interval = 0.38 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: 0.223 AC: 33871 AN: 152012 Hom.: 4044 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.223 AC: 33928 AN: 152130 Hom.: 4063 Cov.: 33 AF XY: 0.221 AC XY: 16438 AN XY: 74384

African (AFR) AF: 0.285 AC: 11807 AN: 41484

American (AMR) AF: 0.239 AC: 3650 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2042 AN: 5184

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4822

European-Finnish (FIN) AF: 0.128 AC: 1353 AN: 10594

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12630 AN: 67968

Other (OTH) AF: 0.218 AC: 460 AN: 2110

Alfa AF: 0.193 Hom.: 4815

Bravo AF: 0.232

Asia WGS AF: 0.312 AC: 1086 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	7.3
DANN	Benign	0.76
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10819634; hg19: chr9-101860076;