rs1931619

Variant names:

• chr6-81915952-G-A
• rs1931619
• ENST00000418567.2:n.195+12905C>T

Variant summary

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

The ENST00000418567.2(LINC02542):​n.195+12905C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,934 control chromosomes in the GnomAD database, including 4,491 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 0.23 (4491 hom., cov: 30)
• Consequence: LINC02542 ENST00000418567.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02542	NR_149134.1	n.146+12905C>T		intron_variant	Intron 2 of 2
LINC02542	NR_149135.1	n.343-70043C>T		intron_variant	Intron 3 of 3
LINC02542	NR_149136.1	n.97+12905C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02542	ENST00000418567.2	n.195+12905C>T		intron_variant	Intron 2 of 2	5
LINC02542	ENST00000660534.3	n.187+22369C>T		intron_variant	Intron 1 of 1
LINC02542	ENST00000660637.1	n.224-70043C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34950 AN: 151816 Hom.: 4494 Cov.: 30

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.230 AC: 34947 AN: 151934 Hom.: 4491 Cov.: 30 AF XY: 0.226 AC XY: 16758 AN XY: 74216

African (AFR) AF: 0.138 AC: 5734 AN: 41484

American (AMR) AF: 0.208 AC: 3178 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3466

East Asian (EAS) AF: 0.0804 AC: 411 AN: 5110

South Asian (SAS) AF: 0.173 AC: 832 AN: 4804

European-Finnish (FIN) AF: 0.252 AC: 2663 AN: 10578

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20157 AN: 67928

Other (OTH) AF: 0.276 AC: 583 AN: 2112

Alfa AF: 0.260 Hom.: 890

Bravo AF: 0.225

Asia WGS AF: 0.117 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.77
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1931619; hg19: chr6-82625669;