rs10517079

Variant names:

• chr4-43480264-A-G
• rs10517079
• ENST00000508563.1:n.108+12172T>C

Variant summary

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

The ENST00000508563.1(LINC02383):​n.108+12172T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.046 in 152,134 control chromosomes in the GnomAD database, including 233 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 0.046 (233 hom., cov: 32)
• Consequence: LINC02383 ENST00000508563.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 0 publications found

Genes affected

LINC02383 (HGNC:53306): (long intergenic non-protein coding RNA 2383)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02383	NR_146993.1	n.108+12172T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02383	ENST00000508563.1	n.108+12172T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0461 AC: 7006 AN: 152016 Hom.: 234 Cov.: 32

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0460 AC: 6999 AN: 152134 Hom.: 233 Cov.: 32 AF XY: 0.0437 AC XY: 3254 AN XY: 74394

African (AFR) AF: 0.0114 AC: 474 AN: 41568

American (AMR) AF: 0.0483 AC: 735 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3468

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5172

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4828

European-Finnish (FIN) AF: 0.0335 AC: 355 AN: 10612

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0689 AC: 4682 AN: 67940

Other (OTH) AF: 0.0582 AC: 123 AN: 2114

Alfa AF: 0.0589 Hom.: 68

Bravo AF: 0.0467

Asia WGS AF: 0.00808 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.73
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10517079; hg19: chr4-43482281;