1-63308530-G-A

Position:

• chr1-63308530-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.340-3784C>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 0.079 in 152,130 control chromosomes in the GnomAD database, including 564 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 0.079 (564 hom., cov: 32)
• Consequence: LINC00466 NR_038252.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00466	NR_038252.3	n.340-3784C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00466	ENST00000656229.1	n.355-3784C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0790 AC: 12014 AN: 152012 Hom.: 563 Cov.: 32

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0790 AC: 12015 AN: 152130 Hom.: 564 Cov.: 32 AF XY: 0.0814 AC XY: 6053 AN XY: 74350

Gnomad4 AFR AF: 0.0508

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.0761

Gnomad4 OTH AF: 0.0867

Alfa AF: 0.0753 Hom.: 809

Bravo AF: 0.0834

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11208184; hg19: chr1-63774201;