20-52588695-C-T

Position:

• chr20-52588695-C-T

Variant summary

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

The ENST00000454600.1(LINC01524):​n.493+38568C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,188 control chromosomes in the GnomAD database, including 2,377 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 0.16 (2377 hom., cov: 32)
• Consequence: LINC01524 ENST00000454600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

LINC01524 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372666	XR_001754670.2	n.893+38568C>T		intron_variant
LOC105372666	XR_007067652.1	n.930+38568C>T		intron_variant
LOC105372666	XR_007067653.1	n.256+38568C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01524	ENST00000454600.1	n.493+38568C>T		intron_variant		3
LINC01524	ENST00000655073.1	n.665-8102C>T		intron_variant
LINC01524	ENST00000656362.1	n.721+38568C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23643 AN: 152070 Hom.: 2377 Cov.: 32

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.155 AC: 23633 AN: 152188 Hom.: 2377 Cov.: 32 AF XY: 0.149 AC XY: 11093 AN XY: 74400

Gnomad4 AFR AF: 0.0504

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0545

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.178

Alfa AF: 0.120 Hom.: 339

Bravo AF: 0.151

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17733118; hg19: chr20-51205234;