3-148669069-A-T

Variant names:

• chr3-148669069-A-T
• rs2012052

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.262 AC: 10867 AN: 41494

American (AMR) AF: 0.782 AC: 11954 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2776 AN: 3472

East Asian (EAS) AF: 0.897 AC: 4635 AN: 5168

South Asian (SAS) AF: 0.639 AC: 3078 AN: 4818

European-Finnish (FIN) AF: 0.814 AC: 8627 AN: 10598

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53389 AN: 67988

Other (OTH) AF: 0.671 AC: 1419 AN: 2116

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2012052; hg19: chr3-148386856;