rs10819634

chr9-99097794-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.218

Alfa AF: 0.191 Hom.: 3737

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10819634; hg19: chr9-101860076;