6-76581444-C-T

Variant names:

• chr6-76581444-C-T
• rs4706623
• ENST00000455554.2:n.216+5004G>A

Variant summary

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

The ENST00000455554.2(LINC02540):​n.216+5004G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,232 control chromosomes in the GnomAD database, including 35,307 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 0.68 (35307 hom., cov: 30)
• Consequence: LINC02540 ENST00000455554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 2 publications found

Genes affected

LINC02540 (HGNC:53573): (long intergenic non-protein coding RNA 2540)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02540	NR_149101.1	n.216+5004G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02540	ENST00000455554.2	n.216+5004G>A		intron_variant	Intron 2 of 2	3
LINC02540	ENST00000653622.1	n.153+5004G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.681 AC: 102982 AN: 151114 Hom.: 35288 Cov.: 30

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.681 AC: 103050 AN: 151232 Hom.: 35307 Cov.: 30 AF XY: 0.686 AC XY: 50679 AN XY: 73860

African (AFR) AF: 0.700 AC: 28943 AN: 41322

American (AMR) AF: 0.704 AC: 10634 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2096 AN: 3448

East Asian (EAS) AF: 0.927 AC: 4735 AN: 5108

South Asian (SAS) AF: 0.738 AC: 3544 AN: 4804

European-Finnish (FIN) AF: 0.696 AC: 7336 AN: 10544

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43642 AN: 67594

Other (OTH) AF: 0.672 AC: 1416 AN: 2106

Alfa AF: 0.661 Hom.: 139497

Bravo AF: 0.687

Asia WGS AF: 0.811 AC: 2820 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs4706623; hg19: chr6-77291161;