12-102639843-A-G

Variant names:

• chr12-102639843-A-G
• rs703582
• ENST00000737486.1:n.122-50263A>G

Variant summary

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

The ENST00000737486.1(ENSG00000296233):​n.122-50263A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.917 in 152,256 control chromosomes in the GnomAD database, including 64,020 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 0.92 (64020 hom., cov: 32)
• Consequence: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 1 publications found

Genes affected

ENSG00000296233 (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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737486.1. 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
	ENSG00000296233	ENST00000737486.1		n.122-50263A>G		intron	N/A
	ENSG00000296233	ENST00000737487.1		n.122-50263A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.917 AC: 139487 AN: 152138 Hom.: 63969 Cov.: 32

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.908

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

GnomAD4 genome AF: 0.917 AC: 139596 AN: 152256 Hom.: 64020 Cov.: 32 AF XY: 0.919 AC XY: 68391 AN XY: 74458

African (AFR) AF: 0.936 AC: 38908 AN: 41558

American (AMR) AF: 0.904 AC: 13822 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3189 AN: 3470

East Asian (EAS) AF: 0.982 AC: 5096 AN: 5188

South Asian (SAS) AF: 0.923 AC: 4452 AN: 4824

European-Finnish (FIN) AF: 0.913 AC: 9665 AN: 10590

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61542 AN: 68008

Other (OTH) AF: 0.908 AC: 1920 AN: 2114

Alfa AF: 0.911 Hom.: 3472

Bravo AF: 0.914

Asia WGS AF: 0.955 AC: 3319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.62
PhyloP100		-2.9

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: rs703582;

hg19: chr12-103033621;