chr13-69306014-T-G

Position:

• chr13-69306014-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00383 (HGNC:):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00383	NR_125752.1	n.229-5321T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00383	ENST00000648574.1	n.251-5321T>G		intron_variant
LINC00383	ENST00000657223.1	n.770-15331T>G		intron_variant

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

Gnomad4 AFR AF: 0.0405

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.106

Alfa AF: 0.133 Hom.: 2789

Bravo AF: 0.100

Asia WGS AF: 0.0870 AC: 303 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17605645; hg19: chr13-69880146;