9-134548366-T-C

Variant names:

• chr9-134548366-T-C
• rs3132306

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 0.31 in 152,016 control chromosomes in the GnomAD database, including 7,491 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 0.31 (7491 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 18 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 (SAS) allele frequency at 95% confidence interval = 0.423 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: 0.311 AC: 47170 AN: 151898 Hom.: 7492 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.310 AC: 47181 AN: 152016 Hom.: 7491 Cov.: 32 AF XY: 0.307 AC XY: 22817 AN XY: 74294

African (AFR) AF: 0.294 AC: 12195 AN: 41458

American (AMR) AF: 0.307 AC: 4689 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1306 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1048 AN: 5154

South Asian (SAS) AF: 0.438 AC: 2109 AN: 4812

European-Finnish (FIN) AF: 0.211 AC: 2229 AN: 10568

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22511 AN: 67956

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.320 Hom.: 18067

Bravo AF: 0.314

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.70
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs3132306; hg19: chr9-137440212;