1-63301926-G-A

Position:

• chr1-63301926-G-A

Variant summary

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

The NR_038252.3(LINC00466):​n.391+2769C>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 0.0827 in 152,228 control chromosomes in the GnomAD database, including 567 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 0.083 (567 hom., cov: 31)
• Consequence: LINC00466 NR_038252.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

Genes affected

LINC00466 (HGNC:27294): (long intergenic non-protein coding RNA 466)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00466	NR_038252.3	n.391+2769C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00466	ENST00000656229.1	n.406+2769C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0828 AC: 12591 AN: 152110 Hom.: 566 Cov.: 31

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0789

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.0311

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0827 AC: 12595 AN: 152228 Hom.: 567 Cov.: 31 AF XY: 0.0785 AC XY: 5841 AN XY: 74430

Gnomad4 AFR AF: 0.0470

Gnomad4 AMR AF: 0.0794

Gnomad4 ASJ AF: 0.0799

Gnomad4 EAS AF: 0.0309

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0626

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.106 Hom.: 506

Bravo AF: 0.0812

Asia WGS AF: 0.0800 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12747934; hg19: chr1-63767597;