ENST00000454600.1:n.493+2328C>A

Variant names:

• chr20-52552455-C-A
• rs2143942
• ENST00000454600.1:n.493+2328C>A

Variant summary

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

The ENST00000454600.1(LINC01524):​n.493+2328C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,032 control chromosomes in the GnomAD database, including 28,374 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 0.59 (28374 hom., cov: 32)
• Consequence: LINC01524 ENST00000454600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 4 publications found

Genes affected

LINC01524 (HGNC:51228): (long intergenic non-protein coding RNA 1524)

LOC105372666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372666	XR_001754670.2	n.893+2328C>A		intron_variant	Intron 6 of 11
LOC105372666	XR_001754671.2	n.893+2328C>A		intron_variant	Intron 6 of 6
LOC105372666	XR_007067652.1	n.930+2328C>A		intron_variant	Intron 7 of 16
LOC105372666	XR_007067653.1	n.256+2328C>A		intron_variant	Intron 2 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01524	ENST00000454600.1	n.493+2328C>A		intron_variant	Intron 6 of 6	3
LINC01524	ENST00000655073.2	n.664+2328C>A		intron_variant	Intron 4 of 4
LINC01524	ENST00000656362.1	n.721+2328C>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89019 AN: 151914 Hom.: 28385 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.586 AC: 89017 AN: 152032 Hom.: 28374 Cov.: 32 AF XY: 0.590 AC XY: 43846 AN XY: 74298

African (AFR) AF: 0.310 AC: 12871 AN: 41454

American (AMR) AF: 0.651 AC: 9955 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2466 AN: 3470

East Asian (EAS) AF: 0.661 AC: 3400 AN: 5144

South Asian (SAS) AF: 0.616 AC: 2964 AN: 4814

European-Finnish (FIN) AF: 0.746 AC: 7897 AN: 10580

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.698 AC: 47475 AN: 67968

Other (OTH) AF: 0.601 AC: 1271 AN: 2114

Alfa AF: 0.656 Hom.: 91322

Bravo AF: 0.570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.52
DANN	Benign	0.54
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs2143942; hg19: chr20-51168994;