rs10819795

Variant names:

• chr9-100606081-T-A
• rs10819795

Your query was ambiguous. Multiple possible variants found:

• chr9-100606081-T-A
• chr9-100606081-T-C

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 0.0425 in 152,164 control chromosomes in the GnomAD database, including 291 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 0.042 (291 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 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: 0.0425 AC: 6467 AN: 152046 Hom.: 292 Cov.: 33

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0228

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0425 AC: 6460 AN: 152164 Hom.: 291 Cov.: 33 AF XY: 0.0467 AC XY: 3470 AN XY: 74374

African (AFR) AF: 0.0430 AC: 1784 AN: 41524

American (AMR) AF: 0.0310 AC: 474 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3472

East Asian (EAS) AF: 0.207 AC: 1067 AN: 5160

South Asian (SAS) AF: 0.200 AC: 964 AN: 4818

European-Finnish (FIN) AF: 0.0432 AC: 458 AN: 10596

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0228 AC: 1547 AN: 67986

Other (OTH) AF: 0.0374 AC: 79 AN: 2112

Alfa AF: 0.0120 Hom.: 5

Bravo AF: 0.0390

Asia WGS AF: 0.206 AC: 713 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.40
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs10819795; hg19: chr9-103368363;