rs4501026

Variant names:

• chr21-28074893-C-A
• rs4501026
• ENST00000458316.2:n.100+26356C>A

Your query was ambiguous. Multiple possible variants found:

• chr21-28074893-C-A
• chr21-28074893-C-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+26356C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,670 control chromosomes in the GnomAD database, including 29,328 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 0.62 (29328 hom., cov: 29)
• Consequence: LINC01697 ENST00000458316.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01697	NR_126010.1		n.124+26356C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01697	ENST00000458316.2	TSL:1	n.100+26356C>A		intron	N/A
	LINC01697	ENST00000426534.2	TSL:2	n.134+26356C>A		intron	N/A
	LINC01697	ENST00000763451.1		n.95+26356C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.620 AC: 93981 AN: 151552 Hom.: 29327 Cov.: 29

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.620 AC: 94021 AN: 151670 Hom.: 29328 Cov.: 29 AF XY: 0.619 AC XY: 45852 AN XY: 74112

African (AFR) AF: 0.604 AC: 24990 AN: 41342

American (AMR) AF: 0.593 AC: 9033 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2279 AN: 3466

East Asian (EAS) AF: 0.687 AC: 3523 AN: 5130

South Asian (SAS) AF: 0.514 AC: 2471 AN: 4806

European-Finnish (FIN) AF: 0.657 AC: 6901 AN: 10510

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.628 AC: 42667 AN: 67888

Other (OTH) AF: 0.604 AC: 1265 AN: 2096

Alfa AF: 0.616 Hom.: 37882

Bravo AF: 0.619

Asia WGS AF: 0.618 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs4501026; hg19: chr21-29447212;