rs2050456

Positions:

• chr9-32597017-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0475

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.129

Alfa AF: 0.153 Hom.: 337

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2050456; hg19: chr9-32597015;