chr12-102556536-C-T

Variant names:

• chr12-102556536-C-T
• rs35765817
• ENST00000737486.1:n.121+12170C>T

Variant summary

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

The ENST00000737486.1(ENSG00000296233):​n.121+12170C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0661 in 152,212 control chromosomes in the GnomAD database, including 331 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 0.066 (331 hom., cov: 32)
• Consequence: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 5 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+72648C>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+12170C>T		intron_variant	Intron 1 of 3
ENSG00000296233	ENST00000737487.1	n.121+12170C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0661 AC: 10052 AN: 152094 Hom.: 332 Cov.: 32

Gnomad AFR AF: 0.0714

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0661 AC: 10066 AN: 152212 Hom.: 331 Cov.: 32 AF XY: 0.0671 AC XY: 4990 AN XY: 74410

African (AFR) AF: 0.0713 AC: 2963 AN: 41532

American (AMR) AF: 0.0710 AC: 1086 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0502 AC: 174 AN: 3468

East Asian (EAS) AF: 0.0802 AC: 416 AN: 5184

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4826

European-Finnish (FIN) AF: 0.0930 AC: 984 AN: 10576

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0606 AC: 4121 AN: 68016

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0621 Hom.: 84

Bravo AF: 0.0655

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.0
DANN	Benign	0.75
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs35765817; hg19: chr12-102950314;