21-28102877-C-T

Variant names:

• chr21-28102877-C-T
• rs9305354
• ENST00000458316.2:n.428C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000458316.2(LINC01697):​n.428C>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 ENST00000458316.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458316.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01697	NR_126011.1		n.501C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC01697	NR_126010.1		n.344+108C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01697	ENST00000458316.2	TSL:1	n.428C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC01697	ENST00000436878.2	TSL:2	n.665C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC01697	ENST00000631186.1	TSL:5	n.474C>T		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.424 AC: 17552 AN: 41356

American (AMR) AF: 0.174 AC: 2651 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0856 AC: 297 AN: 3470

East Asian (EAS) AF: 0.451 AC: 2312 AN: 5128

South Asian (SAS) AF: 0.176 AC: 846 AN: 4816

European-Finnish (FIN) AF: 0.118 AC: 1251 AN: 10586

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9443 AN: 67970

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.173 Hom.: 10664

Bravo AF: 0.244

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.23
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9305354;

hg19: chr21-29475196;