ENST00000637462.1:n.230-12930A>G

Variant names:

• chr13-42371327-A-G
• rs7992970
• ENST00000637462.1:n.230-12930A>G

Variant summary

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

The ENST00000637462.1(LINC02341):​n.230-12930A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,064 control chromosomes in the GnomAD database, including 5,522 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 0.27 (5522 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866
• Publications: 12 publications found

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637462.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637462.1	TSL:5	n.230-12930A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40327 AN: 151944 Hom.: 5512 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.265 AC: 40351 AN: 152064 Hom.: 5522 Cov.: 32 AF XY: 0.267 AC XY: 19842 AN XY: 74334

African (AFR) AF: 0.276 AC: 11455 AN: 41454

American (AMR) AF: 0.224 AC: 3431 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1278 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1760 AN: 5172

South Asian (SAS) AF: 0.393 AC: 1891 AN: 4812

European-Finnish (FIN) AF: 0.267 AC: 2820 AN: 10580

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.247 AC: 16768 AN: 67974

Other (OTH) AF: 0.268 AC: 566 AN: 2110

Alfa AF: 0.250 Hom.: 8389

Bravo AF: 0.260

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.4
DANN	Benign	0.92
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs7992970; hg19: chr13-42945463;