21-28074267-C-T

Variant names:

• chr21-28074267-C-T
• rs2831459
• ENST00000458316.2:n.100+25730C>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+25730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,236 control chromosomes in the GnomAD database, including 63,811 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 0.92 (63811 hom., cov: 33)
• Consequence: LINC01697 ENST00000458316.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.922
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.928 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_126010.1		n.124+25730C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01697	ENST00000458316.2	TSL:1	n.100+25730C>T		intron	N/A
	LINC01697	ENST00000426534.2	TSL:2	n.134+25730C>T		intron	N/A
	LINC01697	ENST00000763451.1		n.95+25730C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139231 AN: 152118 Hom.: 63788 Cov.: 33

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.915 AC: 139308 AN: 152236 Hom.: 63811 Cov.: 33 AF XY: 0.914 AC XY: 68034 AN XY: 74424

African (AFR) AF: 0.880 AC: 36545 AN: 41522

American (AMR) AF: 0.941 AC: 14385 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3253 AN: 3470

East Asian (EAS) AF: 0.849 AC: 4392 AN: 5172

South Asian (SAS) AF: 0.853 AC: 4120 AN: 4828

European-Finnish (FIN) AF: 0.951 AC: 10093 AN: 10610

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.932 AC: 63432 AN: 68026

Other (OTH) AF: 0.906 AC: 1917 AN: 2116

Alfa AF: 0.911 Hom.: 3002

Bravo AF: 0.915

Asia WGS AF: 0.878 AC: 3055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.19
PhyloP100		0.92

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: rs2831459;

hg19: chr21-29446586;