rs17210569

Positions:

• chr13-37948959-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000617568.2(LINC02334):​n.547+13922A>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02334	XR_941880.4	n.590+13922A>T		intron_variant, non_coding_transcript_variant
LINC02334	XR_941877.3	n.590+13922A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02334	ENST00000667295.1	n.442+13922A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.0506

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.0347

Gnomad4 NFE AF: 0.0573

Gnomad4 OTH AF: 0.0445

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17210569; hg19: chr13-38523096;