rs12465765

Variant names:

• chr2-101693058-G-A
• rs12465765

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 0.156 in 152,120 control chromosomes in the GnomAD database, including 2,187 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 (2187 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

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 (EAS) allele frequency at 95% confidence interval = 0.387 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: 0.156 AC: 23683 AN: 152000 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.156 AC: 23680 AN: 152120 Hom.: 2187 Cov.: 32 AF XY: 0.158 AC XY: 11743 AN XY: 74346

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.170

Alfa AF: 0.167 Hom.: 1316

Bravo AF: 0.155

Asia WGS AF: 0.329 AC: 1142 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	2.0
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: rs12465765; hg19: chr2-102309520;