21-28102877-C-T

Position:

• chr21-28102877-C-T

Variant summary

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

The ENST00000458316.1(LINC01697):​n.419C>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 0.23 in 151,916 control chromosomes in the GnomAD database, including 5,414 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 0.23 (5414 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: -2.15

Genes affected

LINC01697 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01697	NR_126011.1	n.501C>T		non_coding_transcript_exon_variant	3/3
LINC01697	NR_126010.1	n.344+108C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01697	ENST00000458316.1	n.419C>T		non_coding_transcript_exon_variant	2/2	1
LINC01697	ENST00000436878.1	n.459C>T		non_coding_transcript_exon_variant	3/3	2
LINC01697	ENST00000631186.1	n.474C>T		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34912 AN: 151798 Hom.: 5400 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.215

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.230 AC: 34965 AN: 151916 Hom.: 5414 Cov.: 32 AF XY: 0.229 AC XY: 16994 AN XY: 74290

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0856

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.214

Alfa AF: 0.157 Hom.: 5376

Bravo AF: 0.244

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9305354; hg19: chr21-29475196;