ENST00000517716.3:n.114-13669G>A

Variant names:

• chr2-46486062-G-A
• rs4953388
• ENST00000517716.3:n.114-13669G>A

Variant summary

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

The ENST00000517716.3(ENSG00000253515):​n.114-13669G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,038 control chromosomes in the GnomAD database, including 7,116 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 0.28 (7116 hom., cov: 32)
• Consequence: ENSG00000253515 ENST00000517716.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 15 publications found

Genes affected

ENSG00000253515 (HGNC:):

LINC02583 (HGNC:53812): (long intergenic non-protein coding RNA 2583)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517716.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253515	ENST00000517716.3	TSL:5	n.114-13669G>A		intron	N/A
	LINC02583	ENST00000843637.1		n.174-41844G>A		intron	N/A
	LINC02583	ENST00000843638.1		n.173+38317G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42187 AN: 151920 Hom.: 7115 Cov.: 32

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.0777

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.277 AC: 42184 AN: 152038 Hom.: 7116 Cov.: 32 AF XY: 0.275 AC XY: 20445 AN XY: 74298

African (AFR) AF: 0.0970 AC: 4025 AN: 41480

American (AMR) AF: 0.343 AC: 5239 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3468

East Asian (EAS) AF: 0.0777 AC: 403 AN: 5188

South Asian (SAS) AF: 0.210 AC: 1014 AN: 4822

European-Finnish (FIN) AF: 0.329 AC: 3468 AN: 10544

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.380 AC: 25815 AN: 67956

Other (OTH) AF: 0.293 AC: 619 AN: 2112

Alfa AF: 0.353 Hom.: 8545

Bravo AF: 0.269

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.49
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4953388; hg19: chr2-46713201;