Variant rs6976 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 ENST00000266014.11(GLT8D1):c.*57G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 1,185,854 control chromosomes in the GnomAD database, including 86,465 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 9497 hom., cov: 33)

Exomes 𝑓: 0.38 ( 76968 hom. )

Consequence

GLT8D1
ENST00000266014.11 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.423

Variant links:

Genes affected

GLT8D1 (HGNC:24870): (glycosyltransferase 8 domain containing 1) This gene encodes a member of the glycosyltransferase family. The specific function of this protein has not been determined. Alternative splicing results in multiple transcript variants of this gene [provided by RefSeq, May 2013]

GLT8D1 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=-0.83).

BP6

Variant 3-52694788-C-T is Benign according to our data. Variant chr3-52694788-C-T is described in ClinVar as [Benign]. Clinvar id is 1224650.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLT8D1	NM_018446.4 linkuse as main transcript	c.*57G>A		3_prime_UTR_variant	10/10	ENST00000266014.11	NP_060916.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLT8D1	ENST00000266014.11 linkuse as main transcript	c.*57G>A		3_prime_UTR_variant	10/10	1	NM_018446.4	ENSP00000266014	P1	Q68CQ7-1

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

50272

AN:

152050

Hom.:

9494

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.460

Gnomad AMR

AF:

0.457

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.427

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.396

Gnomad OTH

AF:

0.357

GnomAD3 exomes

AF:

0.382

AC:

93099

AN:

243900

Hom.:

18966

AF XY:

0.373

AC XY:

49223

AN XY:

131986

show subpopulations

Gnomad AFR exome

AF:

0.142

Gnomad AMR exome

AF:

0.530

Gnomad ASJ exome

AF:

0.450

Gnomad EAS exome

AF:

0.426

Gnomad SAS exome

AF:

0.208

Gnomad FIN exome

AF:

0.404

Gnomad NFE exome

AF:

0.400

Gnomad OTH exome

AF:

0.381

GnomAD4 exome

AF:

0.378

AC:

390224

AN:

1033686

Hom.:

76968

Cov.:

AF XY:

0.371

AC XY:

197900

AN XY:

533282

show subpopulations

Gnomad4 AFR exome

AF:

0.141

Gnomad4 AMR exome

AF:

0.516

Gnomad4 ASJ exome

AF:

0.459

Gnomad4 EAS exome

AF:

0.479

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.401

Gnomad4 NFE exome

AF:

0.387

Gnomad4 OTH exome

AF:

0.357

GnomAD4 genome

AF:

0.331

AC:

50296

AN:

152168

Hom.:

9497

Cov.:

AF XY:

0.333

AC XY:

24739

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.457

Gnomad4 ASJ

AF:

0.449

Gnomad4 EAS

AF:

0.427

Gnomad4 SAS

AF:

0.208

Gnomad4 FIN

AF:

0.391

Gnomad4 NFE

AF:

0.396

Gnomad4 OTH

AF:

0.362

Alfa

AF:

0.387

Hom.:

17490

Bravo

AF:

0.330

Asia WGS

AF:

0.330

AC:

1146

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 12, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.0

DANN

Benign

0.63

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