Genetic Variant GLT8D1:c.646-86_646-83dupTTTA (chr3-52695669-T-TTAAA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018446.4(GLT8D1):c.646-86_646-83dupTTTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 803,842 control chromosomes in the GnomAD database, including 1,257 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.061 ( 342 hom., cov: 31)

Exomes 𝑓: 0.048 ( 915 hom. )

Consequence

GLT8D1
NM_018446.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.194

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 -10 ACMG points.

BP6

Variant 3-52695669-T-TTAAA is Benign according to our data. Variant chr3-52695669-T-TTAAA is described in ClinVar as [Benign]. Clinvar id is 1287305.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLT8D1	NM_018446.4 link	c.646-86_646-83dupTTTA		intron_variant	Intron 7 of 9	ENST00000266014.11	NP_060916.1	Q68CQ7-1A1LQI8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLT8D1	ENST00000266014.11 link	c.646-86_646-83dupTTTA		intron_variant	Intron 7 of 9	1	NM_018446.4	ENSP00000266014.5		Q68CQ7-1

Frequencies

GnomAD3 genomes

AF:

0.0608

AC:

9251

AN:

152178

Hom.:

342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0848

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.0510

Gnomad ASJ

AF:

0.0660

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0124

Gnomad FIN

AF:

0.0295

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0607

Gnomad OTH

AF:

0.0703

GnomAD4 exome

AF:

0.0484

AC:

31537

AN:

651546

Hom.:

915

Cov.:

AF XY:

0.0473

AC XY:

16279

AN XY:

344108

show subpopulations

Gnomad4 AFR exome

AF:

0.0870

Gnomad4 AMR exome

AF:

0.0341

Gnomad4 ASJ exome

AF:

0.0589

Gnomad4 EAS exome

AF:

0.0000560

Gnomad4 SAS exome

AF:

0.0149

Gnomad4 FIN exome

AF:

0.0318

Gnomad4 NFE exome

AF:

0.0576

Gnomad4 OTH exome

AF:

0.0523

GnomAD4 genome

AF:

0.0608

AC:

9258

AN:

152296

Hom.:

342

Cov.:

AF XY:

0.0587

AC XY:

4374

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0848

Gnomad4 AMR

AF:

0.0508

Gnomad4 ASJ

AF:

0.0660

Gnomad4 EAS

AF:

0.000192

Gnomad4 SAS

AF:

0.0126

Gnomad4 FIN

AF:

0.0295

Gnomad4 NFE

AF:

0.0607

Gnomad4 OTH

AF:

0.0695

Alfa

AF:

0.0606

Hom.:

Bravo

AF:

0.0635

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 12, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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