rs2399653

Variant names:

• chr15-97227328-C-A
• rs2399653
• ENST00000559321.2:n.88-8893C>A

Variant summary

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

The ENST00000559321.2(LINC02253):​n.88-8893C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,944 control chromosomes in the GnomAD database, including 3,476 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 0.21 (3476 hom., cov: 32)
• Consequence: LINC02253 ENST00000559321.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 0 publications found

Genes affected

LINC02253 (HGNC:53151): (long intergenic non-protein coding RNA 2253)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559321.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02253	ENST00000559321.2	TSL:2	n.88-8893C>A		intron	N/A
	LINC02253	ENST00000669885.1		n.190+2611C>A		intron	N/A
	LINC02253	ENST00000740177.1		n.390-8893C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31699 AN: 151826 Hom.: 3460 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.209 AC: 31749 AN: 151944 Hom.: 3476 Cov.: 32 AF XY: 0.210 AC XY: 15627 AN XY: 74260

African (AFR) AF: 0.193 AC: 8011 AN: 41444

American (AMR) AF: 0.254 AC: 3868 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3472

East Asian (EAS) AF: 0.376 AC: 1937 AN: 5150

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4820

European-Finnish (FIN) AF: 0.226 AC: 2382 AN: 10548

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13138 AN: 67946

Other (OTH) AF: 0.209 AC: 442 AN: 2110

Alfa AF: 0.123 Hom.: 296

Bravo AF: 0.217

Asia WGS AF: 0.301 AC: 1048 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.83
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2399653; hg19: chr15-97770558;