chr13-42371327-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
LINC02341	ENST00000637462.1	n.230-12930A>G		intron_variant	Intron 2 of 7	5

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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.268

Alfa AF: 0.249 Hom.: 6611

Bravo AF: 0.260

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7992970; hg19: chr13-42945463;