rs9590697

Variant names:

• chr13-42420345-C-G
• rs9590697
• ENST00000637462.1:n.868+8293C>G

Your query was ambiguous. Multiple possible variants found:

• chr13-42420345-C-G
• chr13-42420345-C-T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.868+8293C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,148 control chromosomes in the GnomAD database, including 3,149 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 0.20 (3149 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 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.868+8293C>G		intron_variant	Intron 5 of 7	5

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30043 AN: 152030 Hom.: 3137 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.198 AC: 30076 AN: 152148 Hom.: 3149 Cov.: 32 AF XY: 0.195 AC XY: 14496 AN XY: 74368

African (AFR) AF: 0.157 AC: 6528 AN: 41516

American (AMR) AF: 0.158 AC: 2421 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 972 AN: 3466

East Asian (EAS) AF: 0.168 AC: 874 AN: 5190

South Asian (SAS) AF: 0.291 AC: 1403 AN: 4816

European-Finnish (FIN) AF: 0.176 AC: 1859 AN: 10574

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15276 AN: 67982

Other (OTH) AF: 0.202 AC: 427 AN: 2112

Alfa AF: 0.196 Hom.: 383

Bravo AF: 0.192

Asia WGS AF: 0.260 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.62
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs9590697; hg19: chr13-42994481;