rs35766

Positions:

• chr12-102486695-C-T

Variant summary

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

The XR_007063427.1(LINC02456):​n.34902+2807C>T 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 0.711 in 151,990 control chromosomes in the GnomAD database, including 40,483 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 0.71 (40483 hom., cov: 31)
• Consequence: LINC02456 XR_007063427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

Genes affected

LINC02456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+2807C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108033 AN: 151872 Hom.: 40487 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.711 AC: 108061 AN: 151990 Hom.: 40483 Cov.: 31 AF XY: 0.712 AC XY: 52877 AN XY: 74300

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.730

Alfa AF: 0.806 Hom.: 24317

Bravo AF: 0.695

Asia WGS AF: 0.695 AC: 2415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35766; hg19: chr12-102880473;