rs4291070

Positions:

• chr6-76576927-G-A
• chr6-76576927-G-C
• chr6-76576927-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_149101.1(LINC02540):​n.216+9521C>T variant causes a intron, non coding transcript 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 NR_149101.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02540	NR_149101.1	n.216+9521C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02540	ENST00000653622.1	n.153+9521C>T		intron_variant, non_coding_transcript_variant
LINC02540	ENST00000455554.2	n.216+9521C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.440

Alfa AF: 0.426 Hom.: 6534

Bravo AF: 0.462

Asia WGS AF: 0.592 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4291070; hg19: chr6-77286644;