rs2831462

Variant names:

• chr21-28076177-G-A
• rs2831462
• ENST00000458316.2:n.101-26373G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-28076177-G-A
• chr21-28076177-G-C
• chr21-28076177-G-T

Variant summary

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

The ENST00000458316.2(LINC01697):​n.101-26373G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,986 control chromosomes in the GnomAD database, including 2,514 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 0.17 (2514 hom., cov: 32)
• Consequence: LINC01697 ENST00000458316.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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.125-26373G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01697	ENST00000458316.2	TSL:1	n.101-26373G>A		intron	N/A
	LINC01697	ENST00000426534.2	TSL:2	n.135-26373G>A		intron	N/A
	LINC01697	ENST00000763451.1		n.96-25089G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26155 AN: 151868 Hom.: 2511 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.172 AC: 26166 AN: 151986 Hom.: 2514 Cov.: 32 AF XY: 0.169 AC XY: 12535 AN XY: 74276

African (AFR) AF: 0.245 AC: 10157 AN: 41450

American (AMR) AF: 0.143 AC: 2179 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3472

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5166

South Asian (SAS) AF: 0.0986 AC: 475 AN: 4818

European-Finnish (FIN) AF: 0.145 AC: 1526 AN: 10554

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10732 AN: 67950

Other (OTH) AF: 0.197 AC: 417 AN: 2114

Alfa AF: 0.151 Hom.: 2477

Bravo AF: 0.174

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.6
DANN	Benign	0.54
PhyloP100		0.31

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: rs2831462;

hg19: chr21-29448496;