ENST00000423489.1:n.190-588T>A

Variant names:

• chr6-105623376-A-T
• rs2040431
• ENST00000423489.1:n.190-588T>A

Variant summary

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

The ENST00000423489.1(LINC02836):​n.190-588T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,854 control chromosomes in the GnomAD database, including 30,618 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 0.63 (30618 hom., cov: 31)
• Consequence: LINC02836 ENST00000423489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 5 publications found

Genes affected

LINC02836 (HGNC:54370): (long intergenic non-protein coding RNA 2836)

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 (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423489.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02836	ENST00000423489.1	TSL:3	n.190-588T>A		intron	N/A
	LINC02836	ENST00000654953.1		n.335-588T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95183 AN: 151736 Hom.: 30554 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.628 AC: 95305 AN: 151854 Hom.: 30618 Cov.: 31 AF XY: 0.631 AC XY: 46826 AN XY: 74166

African (AFR) AF: 0.743 AC: 30789 AN: 41444

American (AMR) AF: 0.733 AC: 11188 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2385 AN: 3472

East Asian (EAS) AF: 0.569 AC: 2927 AN: 5148

South Asian (SAS) AF: 0.620 AC: 2972 AN: 4790

European-Finnish (FIN) AF: 0.560 AC: 5894 AN: 10518

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.546 AC: 37054 AN: 67894

Other (OTH) AF: 0.654 AC: 1381 AN: 2112

Alfa AF: 0.449 Hom.: 1208

Bravo AF: 0.646

Asia WGS AF: 0.651 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.12

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: rs2040431; hg19: chr6-106071251;