rs12619870

Variant names:

• chr2-151326786-T-A
• rs12619870

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;