20-52666013-A-G

Position:

• chr20-52666013-A-G

Variant summary

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

The ENST00000666751.1(LINC01524):​n.642-706A>G 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 0.285 in 152,052 control chromosomes in the GnomAD database, including 6,653 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 0.28 (6653 hom., cov: 32)
• Consequence: LINC01524 ENST00000666751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372666	XR_007067652.1	n.931-3135A>G		intron_variant, non_coding_transcript_variant
LOC105372666	XR_001754670.2	n.894-3135A>G		intron_variant, non_coding_transcript_variant
LOC105372666	XR_007067653.1	n.257-3135A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01524	ENST00000666751.1	n.642-706A>G		intron_variant, non_coding_transcript_variant
LINC01524	ENST00000656362.1	n.722-3135A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43285 AN: 151936 Hom.: 6648 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.285 AC: 43312 AN: 152052 Hom.: 6653 Cov.: 32 AF XY: 0.289 AC XY: 21502 AN XY: 74298

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.296

Alfa AF: 0.331 Hom.: 3953

Bravo AF: 0.268

Asia WGS AF: 0.293 AC: 1022 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6063858; hg19: chr20-51282552;