rs1342196

chr6-82095575-G-A

Variant summary

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

The NR_149135.1(LINC02542):n.206+5985C>T 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 0.281 in 152,018 control chromosomes in the GnomAD database, including 6,211 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 0.28 (6211 hom., cov: 32)
• Consequence: LINC02542 NR_149135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02542	NR_149135.1	n.206+5985C>T		intron_variant, non_coding_transcript_variant
LOC107986617	XR_001744231.2	n.751-17882G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02542	ENST00000663543.1	n.290-37570C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42703 AN: 151900 Hom.: 6201 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.281 AC: 42746 AN: 152018 Hom.: 6211 Cov.: 32 AF XY: 0.282 AC XY: 20959 AN XY: 74300

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.266

Alfa AF: 0.257 Hom.: 6677

Bravo AF: 0.286

Asia WGS AF: 0.277 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342196; hg19: chr6-82805292;