ENST00000455554.2:n.216+29977C>T

Variant names:

• chr6-76556471-G-A
• rs4235898
• ENST00000455554.2:n.216+29977C>T

Variant summary

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

The ENST00000455554.2(LINC02540):​n.216+29977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 151,968 control chromosomes in the GnomAD database, including 37,604 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 0.69 (37604 hom., cov: 32)
• Consequence: LINC02540 ENST00000455554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.823
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02540	NR_149101.1	n.216+29977C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02540	ENST00000455554.2	n.216+29977C>T		intron_variant	Intron 2 of 2	3
LINC02540	ENST00000653622.1	n.153+29977C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105418 AN: 151850 Hom.: 37564 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.694 AC: 105515 AN: 151968 Hom.: 37604 Cov.: 32 AF XY: 0.694 AC XY: 51561 AN XY: 74264

African (AFR) AF: 0.856 AC: 35509 AN: 41496

American (AMR) AF: 0.704 AC: 10736 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1868 AN: 3468

East Asian (EAS) AF: 0.768 AC: 3950 AN: 5144

South Asian (SAS) AF: 0.699 AC: 3369 AN: 4818

European-Finnish (FIN) AF: 0.616 AC: 6498 AN: 10542

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41461 AN: 67930

Other (OTH) AF: 0.658 AC: 1387 AN: 2108

Alfa AF: 0.635 Hom.: 137484

Bravo AF: 0.706

Asia WGS AF: 0.736 AC: 2557 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs4235898; hg19: chr6-77266188;