rs2312265

Variant names:

• chr3-152847302-A-G
• rs2312265

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 0.312 in 152,176 control chromosomes in the GnomAD database, including 11,544 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 0.31 (11544 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.312 AC: 47385 AN: 152058 Hom.: 11505 Cov.: 33

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.312 AC: 47478 AN: 152176 Hom.: 11544 Cov.: 33 AF XY: 0.309 AC XY: 23014 AN XY: 74394

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.284

Alfa AF: 0.238 Hom.: 929

Bravo AF: 0.339

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2312265; hg19: chr3-152565091;