3-193979321-G-T

Variant names:

• chr3-193979321-G-T
• rs9855415
• ENST00000397645.2:n.76-19360C>A

Variant summary

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

The ENST00000397645.2(LINC02026):​n.76-19360C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,980 control chromosomes in the GnomAD database, including 30,749 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 0.62 (30749 hom., cov: 31)
• Consequence: LINC02026 ENST00000397645.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 3 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 = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000397645.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02026	NR_033944.1		n.76-19360C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02026	ENST00000397645.2	TSL:2	n.76-19360C>A		intron	N/A
	LINC02026	ENST00000736877.1		n.91-20923C>A		intron	N/A
	LINC02026	ENST00000736878.1		n.91-20694C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94839 AN: 151862 Hom.: 30713 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.625 AC: 94929 AN: 151980 Hom.: 30749 Cov.: 31 AF XY: 0.625 AC XY: 46440 AN XY: 74276

African (AFR) AF: 0.783 AC: 32427 AN: 41434

American (AMR) AF: 0.578 AC: 8829 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2023 AN: 3468

East Asian (EAS) AF: 0.892 AC: 4612 AN: 5168

South Asian (SAS) AF: 0.636 AC: 3060 AN: 4808

European-Finnish (FIN) AF: 0.523 AC: 5519 AN: 10546

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36357 AN: 67954

Other (OTH) AF: 0.637 AC: 1345 AN: 2110

Alfa AF: 0.572 Hom.: 89617

Bravo AF: 0.639

Asia WGS AF: 0.722 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.33
PhyloP100		-0.59

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9855415;

hg19: chr3-193697110;