rs1022689

Positions:

• chr20-52207330-T-G

Variant summary

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

The ENST00000656056.1(LINC01524):​n.279+14893T>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 0.685 in 152,106 control chromosomes in the GnomAD database, including 36,206 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 0.69 (36206 hom., cov: 33)
• Consequence: LINC01524 ENST00000656056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01524	ENST00000656056.1	n.279+14893T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104118 AN: 151988 Hom.: 36164 Cov.: 33

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.685 AC: 104221 AN: 152106 Hom.: 36206 Cov.: 33 AF XY: 0.675 AC XY: 50202 AN XY: 74342

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.692

Alfa AF: 0.688 Hom.: 5691

Bravo AF: 0.695

Asia WGS AF: 0.586 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1022689; hg19: chr20-50823869;