rs9548119

Variant names:

• chr13-37957444-T-A
• rs9548119
• ENST00000617568.2:n.547+22407T>A

Variant summary

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

The ENST00000617568.2(LINC02334):​n.547+22407T>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681
• Publications: 8 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=-0.9).
• 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 rank	MANE	Protein	UniProt
LINC02334	XR_941877.3	n.590+22407T>A		intron_variant	Intron 1 of 3
LINC02334	XR_941880.4	n.590+22407T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02334	ENST00000617568.2	n.547+22407T>A		intron_variant	Intron 1 of 4	1
LINC02334	ENST00000657277.1	n.476+22407T>A		intron_variant	Intron 1 of 5
LINC02334	ENST00000664606.1	n.133+22548T>A		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.127 AC: 5258 AN: 41530

American (AMR) AF: 0.265 AC: 4044 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 806 AN: 3466

East Asian (EAS) AF: 0.310 AC: 1608 AN: 5180

South Asian (SAS) AF: 0.202 AC: 971 AN: 4818

European-Finnish (FIN) AF: 0.264 AC: 2778 AN: 10538

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14707 AN: 67772

Other (OTH) AF: 0.213 AC: 448 AN: 2106

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
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs9548119; hg19: chr13-38531581;