13-37957444-T-A

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.

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+22407T>A		intron	N/A
	LINC02334	ENST00000657277.1		n.476+22407T>A		intron	N/A
	LINC02334	ENST00000664606.1		n.133+22548T>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9548119;

hg19: chr13-38531581;