13-42349067-G-C

Variant names:

• chr13-42349067-G-C
• rs17522044
• ENST00000637462.1:n.229+6465G>C

Variant summary

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

The ENST00000637462.1(LINC02341):​n.229+6465G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,176 control chromosomes in the GnomAD database, including 1,366 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 0.13 (1366 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 5 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 = 0.19 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.229+6465G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19774 AN: 152058 Hom.: 1364 Cov.: 32

Gnomad AFR AF: 0.0981

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.130 AC: 19788 AN: 152176 Hom.: 1366 Cov.: 32 AF XY: 0.129 AC XY: 9593 AN XY: 74392

African (AFR) AF: 0.0980 AC: 4068 AN: 41522

American (AMR) AF: 0.138 AC: 2115 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3470

East Asian (EAS) AF: 0.137 AC: 710 AN: 5164

South Asian (SAS) AF: 0.201 AC: 967 AN: 4820

European-Finnish (FIN) AF: 0.118 AC: 1254 AN: 10588

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9727 AN: 68006

Other (OTH) AF: 0.135 AC: 286 AN: 2114

Alfa AF: 0.0618 Hom.: 59

Bravo AF: 0.129

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.75
PhyloP100		0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17522044;

hg19: chr13-42923203;