13-53861102-C-T

Variant names:

• chr13-53861102-C-T
• rs6561750
• ENST00000569422.1:n.433-9363C>T

Variant summary

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

The ENST00000569422.1(LINC00558):​n.433-9363C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,014 control chromosomes in the GnomAD database, including 24,383 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 (24383 hom., cov: 33)
• Consequence: LINC00558 ENST00000569422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673
• Publications: 6 publications found

Genes affected

LINC00558 (HGNC:43702): (long intergenic non-protein coding RNA 558)

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 (SAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00558	NR_047488.1	n.433-9363C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00558	ENST00000569422.1	n.433-9363C>T		intron_variant	Intron 4 of 5	1
LINC00558	ENST00000655355.1	n.480-12350C>T		intron_variant	Intron 4 of 6
LINC00558	ENST00000666941.1	n.253-9363C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84260 AN: 151894 Hom.: 24373 Cov.: 33

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.554 AC: 84288 AN: 152014 Hom.: 24383 Cov.: 33 AF XY: 0.558 AC XY: 41466 AN XY: 74316

African (AFR) AF: 0.376 AC: 15592 AN: 41478

American (AMR) AF: 0.625 AC: 9535 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2281 AN: 5142

South Asian (SAS) AF: 0.681 AC: 3286 AN: 4822

European-Finnish (FIN) AF: 0.609 AC: 6433 AN: 10566

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43174 AN: 67954

Other (OTH) AF: 0.565 AC: 1194 AN: 2112

Alfa AF: 0.503 Hom.: 7628

Bravo AF: 0.544

Asia WGS AF: 0.538 AC: 1870 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	3.5
DANN	Benign	0.69
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs6561750; hg19: chr13-54435237;