3-148038899-G-T

Variant names:

• chr3-148038899-G-T
• rs1841770
• ENST00000649594.1:n.380+339C>A

Variant summary

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

The ENST00000649594.1(ENSG00000285798):​n.380+339C>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 151,578 control chromosomes in the GnomAD database, including 32,756 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 (32756 hom., cov: 31)
• Consequence: ENSG00000285798 ENST00000649594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 18 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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.380+339C>A		intron_variant	Intron 4 of 4
LINC02032	ENST00000733846.1	n.114+2157G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97467 AN: 151460 Hom.: 32695 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.644 AC: 97592 AN: 151578 Hom.: 32756 Cov.: 31 AF XY: 0.654 AC XY: 48433 AN XY: 74064

African (AFR) AF: 0.813 AC: 33677 AN: 41398

American (AMR) AF: 0.611 AC: 9261 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2157 AN: 3464

East Asian (EAS) AF: 0.824 AC: 4238 AN: 5146

South Asian (SAS) AF: 0.768 AC: 3698 AN: 4818

European-Finnish (FIN) AF: 0.638 AC: 6713 AN: 10530

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

European-Non Finnish (NFE) AF: 0.528 AC: 35788 AN: 67758

Other (OTH) AF: 0.635 AC: 1335 AN: 2104

Alfa AF: 0.575 Hom.: 86312

Bravo AF: 0.648

Asia WGS AF: 0.798 AC: 2760 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.091
DANN	Benign	0.29
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs1841770; hg19: chr3-147756686;