rs7964046

Positions:

• chr12-20125332-T-C

Variant summary

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

The NR_146523.1(LINC02468):​n.183+407A>G 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 0.528 in 151,940 control chromosomes in the GnomAD database, including 22,419 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 0.53 (22419 hom., cov: 32)
• Consequence: LINC02468 NR_146523.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

Genes affected

LINC02468 (HGNC:53406): (long intergenic non-protein coding RNA 2468)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02468	NR_146523.1	n.183+407A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02468	ENST00000655042.1	n.468+395A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80184 AN: 151822 Hom.: 22397 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.528 AC: 80255 AN: 151940 Hom.: 22419 Cov.: 32 AF XY: 0.529 AC XY: 39309 AN XY: 74260

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.536

Alfa AF: 0.456 Hom.: 32645

Bravo AF: 0.539

Asia WGS AF: 0.409 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7964046; hg19: chr12-20278266;