chr9-32597017-G-T

Variant names:

• chr9-32597017-G-T
• rs2050456

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 0.145 in 152,206 control chromosomes in the GnomAD database, including 1,756 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 0.15 (1756 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 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: 0.145 AC: 22062 AN: 152088 Hom.: 1754 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.145 AC: 22085 AN: 152206 Hom.: 1756 Cov.: 31 AF XY: 0.145 AC XY: 10772 AN XY: 74436

African (AFR) AF: 0.102 AC: 4228 AN: 41536

American (AMR) AF: 0.154 AC: 2357 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3466

East Asian (EAS) AF: 0.0475 AC: 246 AN: 5182

South Asian (SAS) AF: 0.119 AC: 573 AN: 4830

European-Finnish (FIN) AF: 0.210 AC: 2218 AN: 10578

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11293 AN: 67992

Other (OTH) AF: 0.129 AC: 273 AN: 2114

Alfa AF: 0.152 Hom.: 643

Bravo AF: 0.140

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.80
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs2050456; hg19: chr9-32597015;