3-148684266-A-T

Variant names:

• chr3-148684266-A-T
• rs1492090

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 0.499 in 151,968 control chromosomes in the GnomAD database, including 22,530 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 0.50 (22530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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: 0.499 AC: 75775 AN: 151852 Hom.: 22520 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.422

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.499 AC: 75791 AN: 151968 Hom.: 22530 Cov.: 32 AF XY: 0.506 AC XY: 37621 AN XY: 74282

African (AFR) AF: 0.158 AC: 6574 AN: 41502

American (AMR) AF: 0.663 AC: 10117 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3468

East Asian (EAS) AF: 0.812 AC: 4189 AN: 5162

South Asian (SAS) AF: 0.546 AC: 2632 AN: 4818

European-Finnish (FIN) AF: 0.680 AC: 7185 AN: 10572

Middle Eastern (MID) AF: 0.420 AC: 116 AN: 276

European-Non Finnish (NFE) AF: 0.611 AC: 41502 AN: 67884

Other (OTH) AF: 0.512 AC: 1081 AN: 2110

Alfa AF: 0.538 Hom.: 3030

Bravo AF: 0.489

Asia WGS AF: 0.643 AC: 2219 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.27
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1492090; hg19: chr3-148402053;