13-53861102-C-T

Position:

• chr13-53861102-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00558 (HGNC:):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00558	NR_047488.1	n.433-9363C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00558	ENST00000569422.1	n.433-9363C>T		intron_variant		1
LINC00558	ENST00000655355.1	n.480-12350C>T		intron_variant
LINC00558	ENST00000666941.1	n.253-9363C>T		intron_variant

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

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.565

Alfa AF: 0.537 Hom.: 2901

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6561750; hg19: chr13-54435237;