rs1242541

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.274

Alfa AF: 0.301 Hom.: 3296

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1242541; hg19: chr14-83206037;