rs833718

Positions:

• chr12-102677308-G-A

Variant summary

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

The XR_007063427.1(LINC02456):​n.34903-12798G>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 0.433 in 152,030 control chromosomes in the GnomAD database, including 14,535 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 0.43 (14535 hom., cov: 33)
• Consequence: LINC02456 XR_007063427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

LINC02456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.34903-12798G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65810 AN: 151912 Hom.: 14517 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.433 AC: 65866 AN: 152030 Hom.: 14535 Cov.: 33 AF XY: 0.431 AC XY: 32043 AN XY: 74300

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.462

Alfa AF: 0.469 Hom.: 28393

Bravo AF: 0.433

Asia WGS AF: 0.527 AC: 1830 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
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: rs833718; hg19: chr12-103071086;