21-28187559-G-A

Variant names:

• chr21-28187559-G-A
• rs2831618
• ENST00000453420.5:n.524-17416C>T

Variant summary

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

The ENST00000453420.5(LINC01695):​n.524-17416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,162 control chromosomes in the GnomAD database, including 1,734 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 0.15 (1734 hom., cov: 32)
• Consequence: LINC01695 ENST00000453420.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 1 publications found

Genes affected

LINC01695 (HGNC:52483): (long intergenic non-protein coding RNA 1695)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453420.5. 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
	LINC01695	NR_126012.1		n.524-17416C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01695	ENST00000453420.5	TSL:1	n.524-17416C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22058 AN: 152044 Hom.: 1728 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.145 AC: 22080 AN: 152162 Hom.: 1734 Cov.: 32 AF XY: 0.143 AC XY: 10623 AN XY: 74404

African (AFR) AF: 0.124 AC: 5142 AN: 41512

American (AMR) AF: 0.129 AC: 1968 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3472

East Asian (EAS) AF: 0.00675 AC: 35 AN: 5184

South Asian (SAS) AF: 0.0608 AC: 293 AN: 4822

European-Finnish (FIN) AF: 0.156 AC: 1656 AN: 10584

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11979 AN: 67974

Other (OTH) AF: 0.147 AC: 310 AN: 2112

Alfa AF: 0.131 Hom.: 553

Bravo AF: 0.142

Asia WGS AF: 0.0510 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.1
DANN	Benign	0.62
PhyloP100		0.36

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: rs2831618;

hg19: chr21-29559878;