9-99173949-C-T

Variant names:

• chr9-99173949-C-T
• rs10819641

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 0.136 in 152,154 control chromosomes in the GnomAD database, including 2,129 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 0.14 (2129 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 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: 0.136 AC: 20617 AN: 152036 Hom.: 2122 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.136 AC: 20651 AN: 152154 Hom.: 2129 Cov.: 32 AF XY: 0.138 AC XY: 10236 AN XY: 74400

African (AFR) AF: 0.234 AC: 9717 AN: 41482

American (AMR) AF: 0.165 AC: 2519 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.439 AC: 2265 AN: 5156

South Asian (SAS) AF: 0.128 AC: 616 AN: 4826

European-Finnish (FIN) AF: 0.0704 AC: 746 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0640 AC: 4352 AN: 68014

Other (OTH) AF: 0.127 AC: 269 AN: 2114

Alfa AF: 0.0886 Hom.: 4032

Bravo AF: 0.149

Asia WGS AF: 0.300 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.065
DANN	Benign	0.66
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10819641; hg19: chr9-101936231; COSMIC: COSV60380947;