rs9309292

Variant names:

• chr2-57073333-T-C
• rs9309292

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 0.172 in 152,006 control chromosomes in the GnomAD database, including 2,602 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 0.17 (2602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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: 0.172 AC: 26068 AN: 151888 Hom.: 2591 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0645

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.172 AC: 26126 AN: 152006 Hom.: 2602 Cov.: 32 AF XY: 0.168 AC XY: 12495 AN XY: 74306

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0649

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.164

Alfa AF: 0.145 Hom.: 2131

Bravo AF: 0.184

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9309292; hg19: chr2-57300468;