rs855203

chr12-102564295-C-Achr12-102564295-C-G

Variant summary

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

The XR_007063427.1(LINC02456):n.34902+80407C>A 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 0.89 in 152,074 control chromosomes in the GnomAD database, including 60,297 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 0.89 (60297 hom., cov: 29)
• Consequence: LINC02456 XR_007063427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

LINC02456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.34902+80407C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135278 AN: 151956 Hom.: 60256 Cov.: 29

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.890 AC: 135377 AN: 152074 Hom.: 60297 Cov.: 29 AF XY: 0.893 AC XY: 66380 AN XY: 74334

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.925

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.901

Alfa AF: 0.893 Hom.: 34214

Bravo AF: 0.892

Asia WGS AF: 0.946 AC: 3289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.086
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs855203; hg19: chr12-102958073;