rs1022689

Variant names:

• chr20-52207330-T-G
• rs1022689
• ENST00000656056.1:n.279+14893T>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01524	ENST00000656056.1	n.279+14893T>G		intron_variant	Intron 1 of 3

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;