3-148669069-A-T

Position:

• chr3-148669069-A-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.148669069A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;