rs2831489

chr21-28103172-G-Tchr21-28103172-G-A

Variant summary

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

The ENST00000458316.1(LINC01697):n.714G>T 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 0.0869 in 152,092 control chromosomes in the GnomAD database, including 660 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 0.087 (660 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01697 ENST00000458316.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947

Genes affected

LINC01697 (HGNC:52485): (long intergenic non-protein coding RNA 1697)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01697	NR_126010.1	n.344+403G>T		intron_variant, non_coding_transcript_variant
LINC01697	NR_126011.1	n.796G>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01697	ENST00000458316.1	n.714G>T		non_coding_transcript_exon_variant	2/2	1
LINC01697	ENST00000426534.2	n.354+403G>T		intron_variant, non_coding_transcript_variant		2
LINC01697	ENST00000436878.1	n.754G>T		non_coding_transcript_exon_variant	3/3	2
LINC01697	ENST00000657256.1	n.832G>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.0869 AC: 13211 AN: 151974 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0351

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0715

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0869 AC: 13221 AN: 152092 Hom.: 660 Cov.: 32 AF XY: 0.0855 AC XY: 6353 AN XY: 74314

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0550

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.0351

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0833

Gnomad4 OTH AF: 0.0708

Alfa AF: 0.0902 Hom.: 91

Bravo AF: 0.0846

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.53
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2831489; hg19: chr21-29475491;