chr12-102546405-T-C

Position:

• chr12-102546405-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+62517T>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 0.835 in 152,160 control chromosomes in the GnomAD database, including 53,303 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 0.84 (53303 hom., cov: 31)
• Consequence: LINC02456 XR_007063427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

LINC02456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.34902+62517T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127037 AN: 152042 Hom.: 53268 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.835 AC: 127126 AN: 152160 Hom.: 53303 Cov.: 31 AF XY: 0.837 AC XY: 62282 AN XY: 74372

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.868

Alfa AF: 0.844 Hom.: 10335

Bravo AF: 0.841

Asia WGS AF: 0.932 AC: 3240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35749; hg19: chr12-102940183;