12-102518780-G-A

Variant names:

• chr12-102518780-G-A
• rs35747
• ENST00000758464.1:n.284+4401G>A

Variant summary

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

The ENST00000758464.1(ENSG00000298855):​n.284+4401G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,018 control chromosomes in the GnomAD database, including 39,961 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 (39961 hom., cov: 31)
• Consequence: ENSG00000298855 ENST00000758464.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 19 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 = 0.829 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

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
	ENSG00000298855	ENST00000758464.1		n.284+4401G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107084 AN: 151900 Hom.: 39962 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.788

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: 0.705 AC: 107109 AN: 152018 Hom.: 39961 Cov.: 31 AF XY: 0.706 AC XY: 52458 AN XY: 74310

African (AFR) AF: 0.434 AC: 17965 AN: 41404

American (AMR) AF: 0.768 AC: 11737 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2646 AN: 3472

East Asian (EAS) AF: 0.657 AC: 3395 AN: 5168

South Asian (SAS) AF: 0.761 AC: 3668 AN: 4820

European-Finnish (FIN) AF: 0.792 AC: 8371 AN: 10566

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56783 AN: 67992

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

Alfa AF: 0.796 Hom.: 189480

Bravo AF: 0.688

Asia WGS AF: 0.689 AC: 2394 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	0.37
DANN	Benign	0.69
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs35747;

hg19: chr12-102912558;