6-76576927-G-A

Variant names:

• chr6-76576927-G-A
• rs4291070
• ENST00000455554.2:n.216+9521C>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+9521C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,210 control chromosomes in the GnomAD database, including 16,391 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 0.46 (16391 hom., cov: 32)
• Consequence: LINC02540 ENST00000455554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455554.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02540	NR_149101.1		n.216+9521C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02540	ENST00000455554.2	TSL:3	n.216+9521C>T		intron	N/A
	LINC02540	ENST00000653622.1		n.153+9521C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69327 AN: 151090 Hom.: 16385 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.459 AC: 69372 AN: 151210 Hom.: 16391 Cov.: 32 AF XY: 0.467 AC XY: 34523 AN XY: 73848

African (AFR) AF: 0.463 AC: 19141 AN: 41342

American (AMR) AF: 0.509 AC: 7677 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1489 AN: 3448

East Asian (EAS) AF: 0.748 AC: 3835 AN: 5126

South Asian (SAS) AF: 0.563 AC: 2709 AN: 4808

European-Finnish (FIN) AF: 0.534 AC: 5632 AN: 10554

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27516 AN: 67536

Other (OTH) AF: 0.440 AC: 924 AN: 2098

Alfa AF: 0.425 Hom.: 7278

Bravo AF: 0.462

Asia WGS AF: 0.592 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.2
DANN	Benign	0.59
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs4291070; hg19: chr6-77286644;