rs12465765

Positions:

• chr2-101693058-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;