21-24305169-A-G

Position:

• chr21-24305169-A-G

Variant summary

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

The NR_109963.1(LINC01689):​n.1388T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,124 control chromosomes in the GnomAD database, including 59,800 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 0.86 (59800 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01689 NR_109963.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

LINC01689 (HGNC:52476): (long intergenic non-protein coding RNA 1689)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01689	NR_109963.1	n.1388T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01689	ENST00000416218.1	n.1388T>C		non_coding_transcript_exon_variant	4/4	1
LINC01689	ENST00000642623.1	n.517T>C		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.862 AC: 130994 AN: 152006 Hom.: 59772 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.899

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.862 AC: 131072 AN: 152124 Hom.: 59800 Cov.: 32 AF XY: 0.867 AC XY: 64501 AN XY: 74404

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.942

Gnomad4 ASJ AF: 0.990

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.999

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.900

Alfa AF: 0.918 Hom.: 8238

Bravo AF: 0.841

Asia WGS AF: 0.970 AC: 3372 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	0.54
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1008552; hg19: chr21-25677482;