13-69306014-T-G

Variant names:

• chr13-69306014-T-G
• rs17605645
• ENST00000648574.1:n.251-5321T>G

Variant summary

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

The NR_125752.1(LINC00383):​n.229-5321T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 150,762 control chromosomes in the GnomAD database, including 1,032 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 0.10 (1032 hom., cov: 32)
• Consequence: LINC00383 NR_125752.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 2 publications found

Genes affected

LINC00383 (HGNC:42710): (long intergenic non-protein coding RNA 383)

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 (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125752.1. 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
	LINC00383	NR_125752.1		n.229-5321T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00383	ENST00000648574.1		n.251-5321T>G		intron	N/A
	LINC00383	ENST00000657223.1		n.770-15331T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15644 AN: 150644 Hom.: 1031 Cov.: 32

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.104 AC: 15643 AN: 150762 Hom.: 1032 Cov.: 32 AF XY: 0.102 AC XY: 7540 AN XY: 73700

African (AFR) AF: 0.0405 AC: 1678 AN: 41388

American (AMR) AF: 0.0856 AC: 1289 AN: 15058

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 508 AN: 3444

East Asian (EAS) AF: 0.110 AC: 568 AN: 5142

South Asian (SAS) AF: 0.0742 AC: 357 AN: 4814

European-Finnish (FIN) AF: 0.112 AC: 1184 AN: 10590

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9480 AN: 67032

Other (OTH) AF: 0.106 AC: 221 AN: 2092

Alfa AF: 0.126 Hom.: 4027

Bravo AF: 0.100

Asia WGS AF: 0.0870 AC: 303 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.34
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs17605645; hg19: chr13-69880146;