5-7361867-A-T

Variant names:

• chr5-7361867-A-T
• rs6891243
• ENST00000715908.1:n.370-1587A>T

Variant summary

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

The ENST00000715908.1(LINC02142):​n.370-1587A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,942 control chromosomes in the GnomAD database, including 13,770 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 0.42 (13770 hom., cov: 32)
• Consequence: LINC02142 ENST00000715908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 0 publications found

Genes affected

LINC02142 (HGNC:53002): (long intergenic non-protein coding RNA 2142)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02142	ENST00000715908.1	n.370-1587A>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63800 AN: 151826 Hom.: 13761 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.420 AC: 63821 AN: 151942 Hom.: 13770 Cov.: 32 AF XY: 0.419 AC XY: 31127 AN XY: 74258

African (AFR) AF: 0.393 AC: 16264 AN: 41430

American (AMR) AF: 0.343 AC: 5232 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1016 AN: 5152

South Asian (SAS) AF: 0.409 AC: 1966 AN: 4812

European-Finnish (FIN) AF: 0.485 AC: 5115 AN: 10538

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31380 AN: 67968

Other (OTH) AF: 0.405 AC: 854 AN: 2110

Alfa AF: 0.440 Hom.: 1860

Bravo AF: 0.407

Asia WGS AF: 0.305 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs6891243; hg19: chr5-7361980;