9-8179325-C-T

Variant names:

• chr9-8179325-C-T
• rs4130580

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 0.158 in 151,992 control chromosomes in the GnomAD database, including 1,990 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 0.16 (1990 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.176 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: 0.158 AC: 24042 AN: 151874 Hom.: 1985 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.158 AC: 24072 AN: 151992 Hom.: 1990 Cov.: 31 AF XY: 0.156 AC XY: 11574 AN XY: 74316

African (AFR) AF: 0.174 AC: 7237 AN: 41474

American (AMR) AF: 0.182 AC: 2774 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0926 AC: 321 AN: 3468

East Asian (EAS) AF: 0.180 AC: 930 AN: 5164

South Asian (SAS) AF: 0.167 AC: 805 AN: 4820

European-Finnish (FIN) AF: 0.100 AC: 1064 AN: 10596

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10393 AN: 67910

Other (OTH) AF: 0.154 AC: 324 AN: 2106

Alfa AF: 0.155 Hom.: 6373

Bravo AF: 0.166

Asia WGS AF: 0.202 AC: 701 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	0.39
DANN	Benign	0.63
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4130580; hg19: chr9-8179325; COSMIC: COSV69446233;