rs4708273

Positions:

• chr6-76554566-T-A
• chr6-76554566-T-C
• chr6-76554566-T-G

Variant summary

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

The NR_149101.1(LINC02540):​n.217-31762A>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 0.693 in 152,084 control chromosomes in the GnomAD database, including 37,353 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 (37353 hom., cov: 32)
• Consequence: LINC02540 NR_149101.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02540	NR_149101.1	n.217-31762A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02540	ENST00000653622.1	n.154-31762A>T		intron_variant, non_coding_transcript_variant
LINC02540	ENST00000455554.2	n.217-31762A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105263 AN: 151966 Hom.: 37302 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.693 AC: 105372 AN: 152084 Hom.: 37353 Cov.: 32 AF XY: 0.693 AC XY: 51535 AN XY: 74344

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.658

Alfa AF: 0.660 Hom.: 4197

Bravo AF: 0.704

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4708273; hg19: chr6-77264283;