rs2050456

Variant names:

• chr9-32597017-G-T
• rs2050456

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 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

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;