rs12619870

chr2-151326786-T-A

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 0.0312 in 152,156 control chromosomes in the GnomAD database, including 113 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 0.031 (113 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.690

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0312 AC: 4736 AN: 152038 Hom.: 111 Cov.: 32

Gnomad AFR AF: 0.0389

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.0195

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.0262

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0312 AC: 4751 AN: 152156 Hom.: 113 Cov.: 32 AF XY: 0.0313 AC XY: 2330 AN XY: 74394

Gnomad4 AFR AF: 0.0391

Gnomad4 AMR AF: 0.0193

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.0361

Gnomad4 FIN AF: 0.0195

Gnomad4 NFE AF: 0.0262

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0309 Hom.: 14

Bravo AF: 0.0326

Asia WGS AF: 0.0700 AC: 241 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
Cadd	Benign	15
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12619870; hg19: chr2-152183300;