rs1242541

Variant names:

• chr14-82739693-A-G
• rs1242541
• ENST00000662642.1:n.185-1006A>G

Variant summary

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

The ENST00000662642.1(LINC02301):​n.185-1006A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,044 control chromosomes in the GnomAD database, including 6,438 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 0.29 (6438 hom., cov: 34)
• Consequence: LINC02301 ENST00000662642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 3 publications found

Genes affected

LINC02301 (HGNC:53220): (long intergenic non-protein coding RNA 2301)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.326 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
LINC02301	ENST00000662642.1	n.185-1006A>G		intron_variant	Intron 3 of 4
LINC02301	ENST00000841947.1	n.183-1006A>G		intron_variant	Intron 3 of 5
LINC02301	ENST00000841948.1	n.237-1006A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43569 AN: 151926 Hom.: 6441 Cov.: 34

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.287 AC: 43569 AN: 152044 Hom.: 6438 Cov.: 34 AF XY: 0.289 AC XY: 21497 AN XY: 74310

African (AFR) AF: 0.228 AC: 9470 AN: 41520

American (AMR) AF: 0.334 AC: 5100 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1331 AN: 5058

South Asian (SAS) AF: 0.266 AC: 1285 AN: 4826

European-Finnish (FIN) AF: 0.327 AC: 3468 AN: 10592

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20603 AN: 67976

Other (OTH) AF: 0.274 AC: 579 AN: 2112

Alfa AF: 0.301 Hom.: 3643

Bravo AF: 0.283

Asia WGS AF: 0.238 AC: 826 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.53
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1242541; hg19: chr14-83206037;