Variant chr12-63779870-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000536219.5(RXYLT1):n.29G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 1,570,228 control chromosomes in the GnomAD database, including 1,297 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 395 hom., cov: 32)

Exomes 𝑓: 0.012 ( 902 hom. )

Consequence

RXYLT1
ENST00000536219.5 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.56

Variant links:

Genes affected

RXYLT1 (HGNC:13530): (ribitol xylosyltransferase 1) This gene encodes a type II transmembrane protein that is thought to have glycosyltransferase function. Mutations in this gene result in cobblestone lissencephaly. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]

RXYLT1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 12-63779870-G-A is Benign according to our data. Variant chr12-63779870-G-A is described in ClinVar as [Benign]. Clinvar id is 672804.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	Effect	MANE
RXYLT1	NM_014254.3 linkuse as main transcript	upstream_gene_variant	ENST00000261234.11
RXYLT1	NM_001278237.2 linkuse as main transcript	upstream_gene_variant
RXYLT1	XM_047428079.1 linkuse as main transcript	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000509615.2 linkuse as main transcript	n.238+15611C>T		intron_variant, non_coding_transcript_variant		5
RXYLT1	ENST00000261234.11 linkuse as main transcript			upstream_gene_variant		1	NM_014254.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0424

AC:

6447

AN:

152130

Hom.:

399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0136

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.0877

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.000588

Gnomad OTH

AF:

0.0325

GnomAD4 exome

AF:

0.0117

AC:

16574

AN:

1417990

Hom.:

902

Cov.:

AF XY:

0.0129

AC XY:

9115

AN XY:

705674

show subpopulations

Gnomad4 AFR exome

AF:

0.128

Gnomad4 AMR exome

AF:

0.00769

Gnomad4 ASJ exome

AF:

0.00123

Gnomad4 EAS exome

AF:

0.109

Gnomad4 SAS exome

AF:

0.0728

Gnomad4 FIN exome

AF:

0.0000254

Gnomad4 NFE exome

AF:

0.000401

Gnomad4 OTH exome

AF:

0.0233

GnomAD4 genome

AF:

0.0423

AC:

6444

AN:

152238

Hom.:

395

Cov.:

AF XY:

0.0429

AC XY:

3191

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.0135

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.129

Gnomad4 SAS

AF:

0.0871

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000588

Gnomad4 OTH

AF:

0.0340

Alfa

AF:

0.00192

Hom.:

Bravo

AF:

0.0456

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.0

DANN

Benign

0.80

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over