chr12-102618116-A-G

Variant names:

• chr12-102618116-A-G
• rs703556
• ENST00000737486.1:n.122-71990A>G

Variant summary

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

The ENST00000737486.1(ENSG00000296233):​n.122-71990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0298 in 152,240 control chromosomes in the GnomAD database, including 140 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 0.030 (140 hom., cov: 32)
• Consequence: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 12 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 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.122-71990A>G		intron	N/A
	ENSG00000296233	ENST00000737487.1		n.122-71990A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4531 AN: 152122 Hom.: 139 Cov.: 32

Gnomad AFR AF: 0.00572

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0746

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0239

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0298 AC: 4535 AN: 152240 Hom.: 140 Cov.: 32 AF XY: 0.0349 AC XY: 2596 AN XY: 74420

African (AFR) AF: 0.00589 AC: 245 AN: 41576

American (AMR) AF: 0.0267 AC: 409 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3472

East Asian (EAS) AF: 0.134 AC: 691 AN: 5162

South Asian (SAS) AF: 0.0745 AC: 359 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1103 AN: 10592

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0240 AC: 1629 AN: 68006

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.0277 Hom.: 187

Bravo AF: 0.0237

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.71
PhyloP100		0.26

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: rs703556;

hg19: chr12-103011894;