9-15394349-C-T

Variant names:

• chr9-15394349-C-T
• rs2804996

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 0.884 in 152,200 control chromosomes in the GnomAD database, including 59,736 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 0.88 (59736 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.92 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: 0.884 AC: 134403 AN: 152082 Hom.: 59682 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.884 AC: 134513 AN: 152200 Hom.: 59736 Cov.: 31 AF XY: 0.883 AC XY: 65692 AN XY: 74402

African (AFR) AF: 0.795 AC: 33017 AN: 41516

American (AMR) AF: 0.931 AC: 14229 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2924 AN: 3472

East Asian (EAS) AF: 0.844 AC: 4363 AN: 5172

South Asian (SAS) AF: 0.780 AC: 3755 AN: 4816

European-Finnish (FIN) AF: 0.966 AC: 10246 AN: 10604

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62992 AN: 68016

Other (OTH) AF: 0.886 AC: 1871 AN: 2112

Alfa AF: 0.899 Hom.: 18264

Bravo AF: 0.881

Asia WGS AF: 0.815 AC: 2837 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	0.73
DANN	Benign	0.093
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2804996; hg19: chr9-15394347;