6-82084877-T-C

Position:

• chr6-82084877-T-C

Variant summary

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

The NR_149135.1(LINC02542):​n.207-12632A>G 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 0.756 in 152,078 control chromosomes in the GnomAD database, including 43,626 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 0.76 (43626 hom., cov: 32)
• Consequence: LINC02542 NR_149135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02542	NR_149135.1	n.207-12632A>G		intron_variant, non_coding_transcript_variant
LOC107986617	XR_001744231.2	n.750+15773T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02542	ENST00000663543.1	n.290-26872A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114876 AN: 151958 Hom.: 43590 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.756 AC: 114971 AN: 152078 Hom.: 43626 Cov.: 32 AF XY: 0.757 AC XY: 56275 AN XY: 74306

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.772

Alfa AF: 0.752 Hom.: 84424

Bravo AF: 0.764

Asia WGS AF: 0.756 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1538138; hg19: chr6-82794594;