rs9919733

Positions:

• chr12-102486344-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+2456T>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 0.13 in 152,190 control chromosomes in the GnomAD database, including 2,166 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 0.13 (2166 hom., cov: 32)
• Consequence: LINC02456 XR_007063427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

LINC02456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+2456T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19767 AN: 152072 Hom.: 2151 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0511

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.130 AC: 19840 AN: 152190 Hom.: 2166 Cov.: 32 AF XY: 0.133 AC XY: 9868 AN XY: 74422

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0511

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.0833

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0412

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0563 Hom.: 600

Bravo AF: 0.140

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9919733; hg19: chr12-102880122;