12-102556815-C-T

Variant names:

• chr12-102556815-C-T
• rs35455143
• ENST00000737486.1:n.121+12449C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000737486.1(ENSG00000296233):​n.121+12449C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0361 in 152,158 control chromosomes in the GnomAD database, including 139 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 0.036 (139 hom., cov: 32)
• Consequence: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 3 publications found

Genes affected

ENSG00000296233 (HGNC:):

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0361 (5486/152158) while in subpopulation NFE AF = 0.0447 (3039/67990). AF 95% confidence interval is 0.0434. There are 139 homozygotes in GnomAd4. There are 2714 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 139 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+72927C>T		intron_variant	Intron 11 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296233	ENST00000737486.1	n.121+12449C>T		intron_variant	Intron 1 of 3
ENSG00000296233	ENST00000737487.1	n.121+12449C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0361 AC: 5482 AN: 152040 Hom.: 139 Cov.: 32

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.0868

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0361 AC: 5486 AN: 152158 Hom.: 139 Cov.: 32 AF XY: 0.0365 AC XY: 2714 AN XY: 74408

African (AFR) AF: 0.0239 AC: 994 AN: 41508

American (AMR) AF: 0.0204 AC: 312 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00706 AC: 34 AN: 4818

European-Finnish (FIN) AF: 0.0868 AC: 919 AN: 10582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0447 AC: 3039 AN: 67990

Other (OTH) AF: 0.0227 AC: 48 AN: 2112

Alfa AF: 0.0396 Hom.: 19

Bravo AF: 0.0305

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	12
DANN	Benign	0.63
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs35455143; hg19: chr12-102950593;