6-82096097-A-T

Position:

• chr6-82096097-A-T

Variant summary

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

The NR_149135.1(LINC02542):​n.206+5463T>A 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 0.59 in 152,042 control chromosomes in the GnomAD database, including 26,826 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 0.59 (26826 hom., cov: 32)
• Consequence: LINC02542 NR_149135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816

Genes affected

LINC02542 (HGNC:53576): (long intergenic non-protein coding RNA 2542)

LOC107986617 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02542	NR_149135.1	n.206+5463T>A		intron_variant, non_coding_transcript_variant
LOC107986617	XR_001744231.2	n.751-17360A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02542	ENST00000663543.1	n.290-38092T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89633 AN: 151924 Hom.: 26813 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.590 AC: 89686 AN: 152042 Hom.: 26826 Cov.: 32 AF XY: 0.587 AC XY: 43629 AN XY: 74318

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.605

Alfa AF: 0.478 Hom.: 1278

Bravo AF: 0.584

Asia WGS AF: 0.448 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
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: rs1556778; hg19: chr6-82805814;