rs13197670

Positions:

• chr6-81860167-G-C

Variant summary

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

The NR_149135.1(LINC02542):​n.343-14258C>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 0.0771 in 152,240 control chromosomes in the GnomAD database, including 504 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 0.077 (504 hom., cov: 33)
• Consequence: LINC02542 NR_149135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02542	NR_149135.1	n.343-14258C>G		intron_variant, non_coding_transcript_variant
LINC02542	NR_149134.1	n.147-14258C>G		intron_variant, non_coding_transcript_variant
LINC02542	NR_149136.1	n.98-14258C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02542	ENST00000663543.1	n.357-14258C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11740 AN: 152122 Hom.: 505 Cov.: 33

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.0771 AC: 11744 AN: 152240 Hom.: 504 Cov.: 33 AF XY: 0.0762 AC XY: 5673 AN XY: 74434

Gnomad4 AFR AF: 0.0787

Gnomad4 AMR AF: 0.0641

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.0754

Gnomad4 OTH AF: 0.0889

Alfa AF: 0.0744 Hom.: 52

Bravo AF: 0.0793

Asia WGS AF: 0.127 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13197670; hg19: chr6-82569884;