3-148039433-A-T

Variant names:

• chr3-148039433-A-T
• rs2219328
• ENST00000649594.1:n.290-105T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649594.1(ENSG00000285798):​n.290-105T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,792 control chromosomes in the GnomAD database, including 32,792 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 (32792 hom., cov: 32)
• Consequence: ENSG00000285798 ENST00000649594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 1 publications found

Genes affected

ENSG00000285798 (HGNC:):

LINC02032 (HGNC:52866): (long intergenic non-protein coding RNA 2032)

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 = 0.809 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
ENSG00000285798	ENST00000649594.1	n.290-105T>A		intron_variant	Intron 3 of 4
LINC02032	ENST00000733846.1	n.114+2691A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97573 AN: 151674 Hom.: 32733 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.644 AC: 97696 AN: 151792 Hom.: 32792 Cov.: 32 AF XY: 0.654 AC XY: 48497 AN XY: 74166

African (AFR) AF: 0.812 AC: 33676 AN: 41460

American (AMR) AF: 0.611 AC: 9279 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2158 AN: 3466

East Asian (EAS) AF: 0.830 AC: 4263 AN: 5136

South Asian (SAS) AF: 0.767 AC: 3698 AN: 4824

European-Finnish (FIN) AF: 0.637 AC: 6723 AN: 10552

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35822 AN: 67862

Other (OTH) AF: 0.636 AC: 1340 AN: 2108

Alfa AF: 0.600 Hom.: 3505

Bravo AF: 0.648

Asia WGS AF: 0.800 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.81
DANN	Benign	0.36
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2219328; hg19: chr3-147757220;