rs12747934

Variant names:

• chr1-63301926-G-A
• rs12747934
• ENST00000436475.3:n.365+2769C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000436475.3(LINC00466):​n.365+2769C>T variant causes a intron 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 ENST00000436475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 1 publications found

Genes affected

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

ENSG00000293613 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00466	NR_038252.3	n.391+2769C>T		intron_variant	Intron 3 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00466	ENST00000436475.3	n.365+2769C>T		intron_variant	Intron 3 of 6	5
LINC00466	ENST00000447183.3	n.90+2769C>T		intron_variant	Intron 2 of 6	5
LINC00466	ENST00000455304.6	n.191+2769C>T		intron_variant	Intron 2 of 4	5

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

African (AFR) AF: 0.0470 AC: 1952 AN: 41552

American (AMR) AF: 0.0794 AC: 1213 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3468

East Asian (EAS) AF: 0.0309 AC: 160 AN: 5172

South Asian (SAS) AF: 0.142 AC: 685 AN: 4818

European-Finnish (FIN) AF: 0.0626 AC: 663 AN: 10594

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7394 AN: 68020

Other (OTH) AF: 0.0837 AC: 177 AN: 2114

Alfa AF: 0.105 Hom.: 1458

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs12747934; hg19: chr1-63767597;