13-73595577-T-C

Position:

• chr13-73595577-T-C

Variant summary

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

The XR_942064.1(LOC105370256):​n.129T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,924 control chromosomes in the GnomAD database, including 22,991 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 0.55 (22991 hom., cov: 32)
• Consequence: LOC105370256 XR_942064.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

Genes affected

LOC105370256 (HGNC:):

LINC00393 (HGNC:42721): (long intergenic non-protein coding RNA 393)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370256	XR_942064.1	n.129T>C		non_coding_transcript_exon_variant	2/7
LINC00393	NR_184171.1	n.143-48736A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00393	ENST00000452852.2	n.32-48736A>G		intron_variant, non_coding_transcript_variant		3
LINC00393	ENST00000648624.1	n.131-48736A>G		intron_variant, non_coding_transcript_variant
LINC00393	ENST00000648903.1	n.165-2117A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82861 AN: 151806 Hom.: 22959 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.546 AC: 82946 AN: 151924 Hom.: 22991 Cov.: 32 AF XY: 0.542 AC XY: 40275 AN XY: 74246

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.546

Alfa AF: 0.558 Hom.: 4737

Bravo AF: 0.540

Asia WGS AF: 0.626 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2875661; hg19: chr13-74169714;