rs9548119

chr13-37957444-T-A

Variant summary

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

The ENST00000617568.2(LINC02334):n.547+22407T>A 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 0.203 in 151,850 control chromosomes in the GnomAD database, including 3,414 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 (3414 hom., cov: 32)
• Consequence: LINC02334 ENST00000617568.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02334	XR_941880.4	n.590+22407T>A		intron_variant, non_coding_transcript_variant
LINC02334	XR_941877.3	n.590+22407T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02334	ENST00000667295.1	n.442+22407T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30780 AN: 151732 Hom.: 3402 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.203 AC: 30798 AN: 151850 Hom.: 3414 Cov.: 32 AF XY: 0.207 AC XY: 15350 AN XY: 74212

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.213

Alfa AF: 0.221 Hom.: 2108

Bravo AF: 0.200

Asia WGS AF: 0.289 AC: 1004 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.2
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9548119; hg19: chr13-38531581;