rs9308765

Variant names:

• chr2-118285633-G-A
• rs9308765

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.165 in 152,028 control chromosomes in the GnomAD database, including 2,541 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 0.16 (2541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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: 0.165 AC: 25041 AN: 151910 Hom.: 2534 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.165 AC: 25078 AN: 152028 Hom.: 2541 Cov.: 32 AF XY: 0.164 AC XY: 12156 AN XY: 74320

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0858

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.141

Alfa AF: 0.124 Hom.: 1929

Bravo AF: 0.170

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	13
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9308765; hg19: chr2-119043209;