rs17063218

Variant names:

• chr13-42348123-G-A
• rs17063218
• ENST00000637462.1:n.229+5521G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-42348123-G-A
• chr13-42348123-G-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+5521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 151,570 control chromosomes in the GnomAD database, including 2,171 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 0.17 (2171 hom., cov: 31)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 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.229+5521G>A		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25087 AN: 151452 Hom.: 2167 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.166 AC: 25116 AN: 151570 Hom.: 2171 Cov.: 31 AF XY: 0.164 AC XY: 12120 AN XY: 74034

African (AFR) AF: 0.182 AC: 7495 AN: 41280

American (AMR) AF: 0.166 AC: 2521 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3464

East Asian (EAS) AF: 0.139 AC: 715 AN: 5156

South Asian (SAS) AF: 0.236 AC: 1127 AN: 4774

European-Finnish (FIN) AF: 0.130 AC: 1365 AN: 10488

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10794 AN: 67888

Other (OTH) AF: 0.169 AC: 354 AN: 2098

Alfa AF: 0.153 Hom.: 314

Bravo AF: 0.166

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.43
DANN	Benign	0.43
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs17063218; hg19: chr13-42922259;