3-193981986-G-T

Variant names:

• chr3-193981986-G-T
• rs7649230
• ENST00000736880.1:n.119C>A

Variant summary

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

The ENST00000736880.1(LINC02026):​n.119C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,070 control chromosomes in the GnomAD database, including 16,781 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 0.46 (16781 hom., cov: 33)
• Consequence: LINC02026 ENST00000736880.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 6 publications found

Genes affected

LINC02026 (HGNC:52861): (long intergenic non-protein coding RNA 2026)

ENSG00000238043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02026	NR_033944.1	n.75+21599C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02026	ENST00000736880.1	n.119C>A		non_coding_transcript_exon_variant	Exon 2 of 4
LINC02026	ENST00000736882.1	n.110C>A		non_coding_transcript_exon_variant	Exon 2 of 4
LINC02026	ENST00000736883.1	n.96C>A		non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70207 AN: 151954 Hom.: 16757 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.462 AC: 70284 AN: 152070 Hom.: 16781 Cov.: 33 AF XY: 0.460 AC XY: 34207 AN XY: 74334

African (AFR) AF: 0.557 AC: 23073 AN: 41448

American (AMR) AF: 0.451 AC: 6885 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1223 AN: 3468

East Asian (EAS) AF: 0.685 AC: 3550 AN: 5180

South Asian (SAS) AF: 0.551 AC: 2657 AN: 4820

European-Finnish (FIN) AF: 0.355 AC: 3757 AN: 10580

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27746 AN: 67980

Other (OTH) AF: 0.431 AC: 909 AN: 2110

Alfa AF: 0.431 Hom.: 38787

Bravo AF: 0.474

Asia WGS AF: 0.576 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.78
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7649230; hg19: chr3-193699775;