ENST00000458316.2:n.100+26974C>T

Variant names:

• chr21-28075511-C-T
• rs16981663
• ENST00000458316.2:n.100+26974C>T

Variant summary

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

The ENST00000458316.2(LINC01697):​n.100+26974C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0474 in 152,068 control chromosomes in the GnomAD database, including 370 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 0.047 (370 hom., cov: 32)
• Consequence: LINC01697 ENST00000458316.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 1 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=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01697	NR_126010.1	n.124+26974C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01697	ENST00000458316.2	n.100+26974C>T		intron_variant	Intron 1 of 1	1
LINC01697	ENST00000426534.2	n.134+26974C>T		intron_variant	Intron 1 of 4	2
LINC01697	ENST00000763451.1	n.96-25755C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0474 AC: 7200 AN: 151950 Hom.: 370 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0430

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0474 AC: 7208 AN: 152068 Hom.: 370 Cov.: 32 AF XY: 0.0510 AC XY: 3790 AN XY: 74338

African (AFR) AF: 0.0305 AC: 1264 AN: 41506

American (AMR) AF: 0.146 AC: 2227 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3466

East Asian (EAS) AF: 0.186 AC: 964 AN: 5176

South Asian (SAS) AF: 0.0371 AC: 179 AN: 4820

European-Finnish (FIN) AF: 0.0529 AC: 559 AN: 10568

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0263 AC: 1785 AN: 67972

Other (OTH) AF: 0.0425 AC: 90 AN: 2116

Alfa AF: 0.0355 Hom.: 265

Bravo AF: 0.0563

Asia WGS AF: 0.0830 AC: 288 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	18
DANN	Benign	0.54
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs16981663; hg19: chr21-29447830;