20-52666556-C-T

Position:

• chr20-52666556-C-T

Variant summary

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

The ENST00000666751.1(LINC01524):​n.642-163C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 152,212 control chromosomes in the GnomAD database, including 62,961 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 0.91 (62961 hom., cov: 31)
• Consequence: LINC01524 ENST00000666751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

Genes affected

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

LOC105372666 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372666	XR_007067652.1	n.931-2592C>T		intron_variant, non_coding_transcript_variant
LOC105372666	XR_001754670.2	n.894-2592C>T		intron_variant, non_coding_transcript_variant
LOC105372666	XR_007067653.1	n.257-2592C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01524	ENST00000666751.1	n.642-163C>T		intron_variant, non_coding_transcript_variant
LINC01524	ENST00000656362.1	n.722-2592C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138058 AN: 152094 Hom.: 62897 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.908 AC: 138182 AN: 152212 Hom.: 62961 Cov.: 31 AF XY: 0.906 AC XY: 67393 AN XY: 74412

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.913

Alfa AF: 0.895 Hom.: 82741

Bravo AF: 0.907

Asia WGS AF: 0.863 AC: 3003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs707544; hg19: chr20-51283095;