3-148669069-A-T

Variant names:

• chr3-148669069-A-T
• rs2012052

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 0.642 in 152,146 control chromosomes in the GnomAD database, including 35,757 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 0.64 (35757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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: 0.642 AC: 97594 AN: 152028 Hom.: 35747 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.642 AC: 97616 AN: 152146 Hom.: 35757 Cov.: 32 AF XY: 0.648 AC XY: 48161 AN XY: 74374

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.671

Alfa AF: 0.580 Hom.: 2009

Bravo AF: 0.629

Asia WGS AF: 0.714 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2012052; hg19: chr3-148386856;