rs10517079

chr4-43480264-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146993.1(LINC02383):n.108+12172T>C variant causes a intron, non coding transcript 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 NR_146993.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02383	NR_146993.1	n.108+12172T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02383	ENST00000508563.1	n.108+12172T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0114

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.0335

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0562 Hom.: 26

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517079; hg19: chr4-43482281;