12-102546405-T-C

Variant names:

• chr12-102546405-T-C
• rs35749
• ENST00000737486.1:n.121+2039T>C

Variant summary

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

The ENST00000737486.1(ENSG00000296233):​n.121+2039T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,160 control chromosomes in the GnomAD database, including 53,303 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 0.84 (53303 hom., cov: 31)
• Consequence: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296233	ENST00000737486.1		n.121+2039T>C		intron	N/A
	ENSG00000296233	ENST00000737487.1		n.121+2039T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127037 AN: 152042 Hom.: 53268 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.835 AC: 127126 AN: 152160 Hom.: 53303 Cov.: 31 AF XY: 0.837 AC XY: 62282 AN XY: 74372

African (AFR) AF: 0.763 AC: 31647 AN: 41480

American (AMR) AF: 0.899 AC: 13743 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2932 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4896 AN: 5184

South Asian (SAS) AF: 0.876 AC: 4220 AN: 4816

European-Finnish (FIN) AF: 0.820 AC: 8680 AN: 10584

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58175 AN: 68018

Other (OTH) AF: 0.868 AC: 1832 AN: 2110

Alfa AF: 0.842 Hom.: 10569

Bravo AF: 0.841

Asia WGS AF: 0.932 AC: 3240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.35
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs35749; hg19: chr12-102940183;