12-116453351-T-C

Variant names:

• chr12-116453351-T-C
• rs10774863
• ENST00000739862.1:n.109+10184T>C

Variant summary

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

The ENST00000739862.1(LINC02457):​n.109+10184T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,104 control chromosomes in the GnomAD database, including 9,912 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 0.36 (9912 hom., cov: 32)
• Consequence: LINC02457 ENST00000739862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02457	ENST00000739862.1		n.109+10184T>C		intron	N/A
	ENSG00000296503	ENST00000739961.1		n.286-9283T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54275 AN: 151986 Hom.: 9900 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.357 AC: 54307 AN: 152104 Hom.: 9912 Cov.: 32 AF XY: 0.356 AC XY: 26486 AN XY: 74370

African (AFR) AF: 0.294 AC: 12220 AN: 41504

American (AMR) AF: 0.324 AC: 4944 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1675 AN: 3464

East Asian (EAS) AF: 0.470 AC: 2427 AN: 5162

South Asian (SAS) AF: 0.488 AC: 2354 AN: 4826

European-Finnish (FIN) AF: 0.336 AC: 3553 AN: 10576

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25920 AN: 67976

Other (OTH) AF: 0.383 AC: 811 AN: 2116

Alfa AF: 0.375 Hom.: 42584

Bravo AF: 0.349

Asia WGS AF: 0.445 AC: 1548 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	0.25
DANN	Benign	0.71
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs10774863; hg19: chr12-116891156;