12-102497908-T-C

Position:

• chr12-102497908-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007063427.1(LINC02456):​n.34902+14020T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,196 control chromosomes in the GnomAD database, including 2,399 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 0.14 (2399 hom., cov: 32)
• Consequence: LINC02456 XR_007063427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

LINC02456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.34902+14020T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20657 AN: 152078 Hom.: 2380 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.136 AC: 20731 AN: 152196 Hom.: 2399 Cov.: 32 AF XY: 0.138 AC XY: 10262 AN XY: 74396

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.0844

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0535 Hom.: 748

Bravo AF: 0.147

Asia WGS AF: 0.222 AC: 768 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.10
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7965399; hg19: chr12-102891686;