rs17210569

Variant names:

• chr13-37948959-A-T
• rs17210569
• ENST00000617568.2:n.547+13922A>T

Variant summary

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

The ENST00000617568.2(LINC02334):​n.547+13922A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0383 in 152,352 control chromosomes in the GnomAD database, including 158 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 0.038 (158 hom., cov: 33)
• Consequence: LINC02334 ENST00000617568.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 0 publications found

Genes affected

LINC02334 (HGNC:53254): (long intergenic non-protein coding RNA 2334)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000617568.2. 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
	LINC02334	ENST00000617568.2	TSL:1	n.547+13922A>T		intron	N/A
	LINC02334	ENST00000657277.1		n.476+13922A>T		intron	N/A
	LINC02334	ENST00000664606.1		n.133+14063A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0384 AC: 5847 AN: 152234 Hom.: 158 Cov.: 33

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0383 AC: 5842 AN: 152352 Hom.: 158 Cov.: 33 AF XY: 0.0377 AC XY: 2809 AN XY: 74504

African (AFR) AF: 0.0105 AC: 436 AN: 41586

American (AMR) AF: 0.0506 AC: 774 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4830

European-Finnish (FIN) AF: 0.0347 AC: 369 AN: 10626

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0573 AC: 3896 AN: 68030

Other (OTH) AF: 0.0445 AC: 94 AN: 2114

Alfa AF: 0.0444 Hom.: 21

Bravo AF: 0.0381

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.76
DANN	Benign	0.63
PhyloP100		-0.44

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: rs17210569;

hg19: chr13-38523096;