ENST00000739862.1:n.109+2841G>A

Variant names:

• chr12-116446008-G-A
• rs1566929
• ENST00000739862.1:n.109+2841G>A

Variant summary

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

The ENST00000739862.1(LINC02457):​n.109+2841G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,076 control chromosomes in the GnomAD database, including 11,294 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 0.38 (11294 hom., cov: 33)
• Consequence: LINC02457 ENST00000739862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 1 publications found

Genes affected

LINC02457 (HGNC:53393): (long intergenic non-protein coding RNA 2457)

ENSG00000296503 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739862.1. 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
	LINC02457	ENST00000739862.1		n.109+2841G>A		intron	N/A
	ENSG00000296503	ENST00000739961.1		n.285+6655G>A		intron	N/A
	ENSG00000296503	ENST00000739962.1		n.269-2506G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58094 AN: 151958 Hom.: 11281 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.382 AC: 58135 AN: 152076 Hom.: 11294 Cov.: 33 AF XY: 0.381 AC XY: 28294 AN XY: 74344

African (AFR) AF: 0.322 AC: 13364 AN: 41482

American (AMR) AF: 0.340 AC: 5190 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3466

East Asian (EAS) AF: 0.462 AC: 2389 AN: 5172

South Asian (SAS) AF: 0.474 AC: 2284 AN: 4822

European-Finnish (FIN) AF: 0.386 AC: 4086 AN: 10576

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.411 AC: 27952 AN: 67970

Other (OTH) AF: 0.398 AC: 842 AN: 2116

Alfa AF: 0.401 Hom.: 11772

Bravo AF: 0.374

Asia WGS AF: 0.437 AC: 1518 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.20
DANN	Benign	0.76
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1566929; hg19: chr12-116883813;