rs9533095

Variant names:

• chr13-42394913-G-T
• rs9533095
• ENST00000637462.1:n.711+310G>T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.711+310G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,060 control chromosomes in the GnomAD database, including 12,595 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 0.39 (12595 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 22 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 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.711+310G>T		intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59226 AN: 151942 Hom.: 12595 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.390 AC: 59241 AN: 152060 Hom.: 12595 Cov.: 32 AF XY: 0.388 AC XY: 28819 AN XY: 74344

African (AFR) AF: 0.265 AC: 10973 AN: 41468

American (AMR) AF: 0.394 AC: 6021 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3470

East Asian (EAS) AF: 0.0854 AC: 442 AN: 5178

South Asian (SAS) AF: 0.281 AC: 1356 AN: 4818

European-Finnish (FIN) AF: 0.527 AC: 5569 AN: 10566

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32387 AN: 67956

Other (OTH) AF: 0.391 AC: 827 AN: 2116

Alfa AF: 0.435 Hom.: 23186

Bravo AF: 0.379

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.62
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs9533095; hg19: chr13-42969049;