ENST00000397645.2:n.76-19360C>A

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02026	NR_033944.1	n.76-19360C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02026	ENST00000397645.2	n.76-19360C>A		intron_variant	Intron 1 of 2	2

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

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.637

Alfa AF: 0.561 Hom.: 35926

Bravo AF: 0.639

Asia WGS AF: 0.722 AC: 2512 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	1.0
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9855415; hg19: chr3-193697110;