rs13197670

Variant names:

• chr6-81860167-G-C
• rs13197670
• ENST00000418567.2:n.196-14258C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000418567.2(LINC02542):​n.196-14258C>G variant causes a intron 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 ENST00000418567.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02542	NR_149134.1	n.147-14258C>G		intron_variant	Intron 2 of 2
LINC02542	NR_149135.1	n.343-14258C>G		intron_variant	Intron 3 of 3
LINC02542	NR_149136.1	n.98-14258C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02542	ENST00000418567.2	n.196-14258C>G		intron_variant	Intron 2 of 2	5
LINC02542	ENST00000658218.1	n.204+27C>G		intron_variant	Intron 1 of 1
LINC02542	ENST00000660534.3	n.188-14258C>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.0787 AC: 3269 AN: 41530

American (AMR) AF: 0.0641 AC: 980 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3470

East Asian (EAS) AF: 0.160 AC: 827 AN: 5176

South Asian (SAS) AF: 0.110 AC: 528 AN: 4818

European-Finnish (FIN) AF: 0.0298 AC: 316 AN: 10616

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0754 AC: 5130 AN: 68018

Other (OTH) AF: 0.0889 AC: 188 AN: 2114

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
PhyloP100		-0.059
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs13197670; hg19: chr6-82569884;