rs4235898

chr6-76556471-G-A

Variant summary

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

The NR_149101.1(LINC02540):n.216+29977C>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 0.694 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 NR_149101.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.823

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=-0.97).
• 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/exons	MANE	UniProt
LINC02540	NR_149101.1	n.216+29977C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02540	ENST00000653622.1	n.153+29977C>T		intron_variant, non_coding_transcript_variant
LINC02540	ENST00000455554.2	n.216+29977C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.658

Alfa AF: 0.618 Hom.: 58597

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4235898; hg19: chr6-77266188;