rs9309292

Variant names:

• chr2-57073333-T-C
• rs9309292

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 0.172 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.267 AC: 11073 AN: 41486

American (AMR) AF: 0.172 AC: 2625 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3468

East Asian (EAS) AF: 0.0649 AC: 336 AN: 5180

South Asian (SAS) AF: 0.206 AC: 992 AN: 4820

European-Finnish (FIN) AF: 0.0717 AC: 759 AN: 10588

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.136 AC: 9245 AN: 67890

Other (OTH) AF: 0.164 AC: 346 AN: 2110

Alfa AF: 0.152 Hom.: 3267

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs9309292; hg19: chr2-57300468;