chr13-42405815-A-G

Variant names:

• chr13-42405815-A-G
• rs7326472
• ENST00000637462.1:n.712-6081A>G

Variant summary

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

The ENST00000637462.1(LINC02341):​n.712-6081A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 152,218 control chromosomes in the GnomAD database, including 917 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 0.10 (917 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 13 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 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.712-6081A>G		intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15180 AN: 152100 Hom.: 916 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.0801

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

GnomAD4 genome AF: 0.0998 AC: 15186 AN: 152218 Hom.: 917 Cov.: 33 AF XY: 0.105 AC XY: 7789 AN XY: 74440

African (AFR) AF: 0.165 AC: 6845 AN: 41506

American (AMR) AF: 0.0529 AC: 810 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3466

East Asian (EAS) AF: 0.146 AC: 754 AN: 5176

South Asian (SAS) AF: 0.189 AC: 911 AN: 4822

European-Finnish (FIN) AF: 0.107 AC: 1131 AN: 10618

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.0587 AC: 3993 AN: 68014

Other (OTH) AF: 0.0811 AC: 171 AN: 2108

Alfa AF: 0.0731 Hom.: 424

Bravo AF: 0.0937

Asia WGS AF: 0.161 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.59
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7326472; hg19: chr13-42979951;