12-102517032-A-G

Variant names:

• chr12-102517032-A-G
• rs855211
• ENST00000758464.1:n.284+2653A>G

Variant summary

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

The ENST00000758464.1(ENSG00000298855):​n.284+2653A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,990 control chromosomes in the GnomAD database, including 39,579 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 0.70 (39579 hom., cov: 31)
• Consequence: ENSG00000298855 ENST00000758464.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 6 publications found

Genes affected

ENSG00000298855 (HGNC:):

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758464.1. 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
	ENSG00000298855	ENST00000758464.1		n.284+2653A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106176 AN: 151872 Hom.: 39581 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.699 AC: 106201 AN: 151990 Hom.: 39579 Cov.: 31 AF XY: 0.700 AC XY: 52012 AN XY: 74278

African (AFR) AF: 0.412 AC: 17078 AN: 41416

American (AMR) AF: 0.766 AC: 11699 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2666 AN: 3470

East Asian (EAS) AF: 0.656 AC: 3390 AN: 5166

South Asian (SAS) AF: 0.761 AC: 3655 AN: 4802

European-Finnish (FIN) AF: 0.792 AC: 8360 AN: 10560

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56809 AN: 67996

Other (OTH) AF: 0.725 AC: 1530 AN: 2110

Alfa AF: 0.798 Hom.: 23524

Bravo AF: 0.681

Asia WGS AF: 0.687 AC: 2389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.47
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs855211; hg19: chr12-102910810;