rs35749

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+62517T>C		intron_variant	Intron 11 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296233	ENST00000737486.1	n.121+2039T>C		intron_variant	Intron 1 of 3
ENSG00000296233	ENST00000737487.1	n.121+2039T>C		intron_variant	Intron 1 of 2

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 v4.3

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;