13-73595577-T-C

Variant names:

• chr13-73595577-T-C
• rs2875661
• XR_942064.1:n.129T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

LOC105370256 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443621.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00393	NR_184171.1		n.143-48736A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00393	ENST00000443621.2	TSL:3	n.136-48736A>G		intron	N/A
	LINC00393	ENST00000452852.2	TSL:3	n.32-48736A>G		intron	N/A
	LINC00393	ENST00000648624.2		n.171-48736A>G		intron	N/A

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

African (AFR) AF: 0.543 AC: 22503 AN: 41404

American (AMR) AF: 0.427 AC: 6528 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2052 AN: 3466

East Asian (EAS) AF: 0.733 AC: 3780 AN: 5156

South Asian (SAS) AF: 0.556 AC: 2671 AN: 4804

European-Finnish (FIN) AF: 0.493 AC: 5203 AN: 10544

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38148 AN: 67958

Other (OTH) AF: 0.546 AC: 1154 AN: 2112

Alfa AF: 0.548 Hom.: 7770

Bravo AF: 0.540

Asia WGS AF: 0.626 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.63
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2875661; hg19: chr13-74169714;