13-93046950-G-C

Position:

• chr13-93046950-G-C

Variant summary

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

The NR_126360.1(LINC00363):​n.32-77G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,080 control chromosomes in the GnomAD database, including 968 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 0.11 (968 hom., cov: 32)
• Consequence: LINC00363 NR_126360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

Genes affected

LINC00363 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00363	NR_126360.1	n.32-77G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00363	ENST00000660073.1	n.337-77G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16658 AN: 151962 Hom.: 963 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0976

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.110 AC: 16681 AN: 152080 Hom.: 968 Cov.: 32 AF XY: 0.113 AC XY: 8414 AN XY: 74330

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.0424

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0976

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0522 Hom.: 44

Bravo AF: 0.110

Asia WGS AF: 0.131 AC: 451 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1444227; hg19: chr13-93699203;