3-52697536-TCTC-T

Position:

• chr3-52697536-TCTC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018446.4(GLT8D1):​c.329+182_329+184delGAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 591,344 control chromosomes in the GnomAD database, including 374 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.033 (273 hom., cov: 32)
  • Exomes 𝑓: 0.0047 (101 hom.)
• Consequence: GLT8D1 NM_018446.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.624

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-52697536-TCTC-T is Benign according to our data. Variant chr3-52697536-TCTC-T is described in ClinVar as [Benign]. Clinvar id is 1278330.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLT8D1	NM_018446.4	c.329+182_329+184delGAG		intron_variant		ENST00000266014.11	NP_060916.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLT8D1	ENST00000266014.11	c.329+182_329+184delGAG		intron_variant		1	NM_018446.4	ENSP00000266014.5

Frequencies

GnomAD3 genomes AF: 0.0331 AC: 5042 AN: 152134 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0146

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000764

Gnomad OTH AF: 0.0282

GnomAD4 exome AF: 0.00471 AC: 2067 AN: 439092 Hom.: 101 AF XY: 0.00402 AC XY: 929 AN XY: 231224

Gnomad4 AFR exome AF: 0.111

Gnomad4 AMR exome AF: 0.0104

Gnomad4 ASJ exome AF: 0.00103

Gnomad4 EAS exome AF: 0.000164

Gnomad4 SAS exome AF: 0.000451

Gnomad4 FIN exome AF: 0.0000697

Gnomad4 NFE exome AF: 0.000636

Gnomad4 OTH exome AF: 0.0107

GnomAD4 genome AF: 0.0332 AC: 5049 AN: 152252 Hom.: 273 Cov.: 32 AF XY: 0.0318 AC XY: 2364 AN XY: 74450

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0146

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.000765

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0251 Hom.: 17

Bravo AF: 0.0380

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs61309926; hg19: chr3-52731552;