3-52695182-CTACT-CTACTTACT

Variant names:

• chr3-52695182-C-CTACT
• rs60069075
• NM_018446.4:c.925+4_925+7dupAGTA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_018446.4(GLT8D1):​c.925+4_925+7dupAGTA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0184 in 1,589,536 control chromosomes in the GnomAD database, including 328 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.015 (21 hom., cov: 32)
  • Exomes 𝑓: 0.019 (307 hom.)
• Consequence: GLT8D1 NM_018446.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.015 (2292/152306) while in subpopulation SAS AF= 0.036 (174/4828). AF 95% confidence interval is 0.0317. There are 21 homozygotes in gnomad4. There are 1117 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 21 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLT8D1	NM_018446.4	c.925+4_925+7dupAGTA		splice_region_variant, intron_variant	Intron 9 of 9	ENST00000266014.11	NP_060916.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLT8D1	ENST00000266014.11	c.925+7_925+8insAGTA		splice_region_variant, intron_variant	Intron 9 of 9	1	NM_018446.4	ENSP00000266014.5

Frequencies

GnomAD3 genomes AF: 0.0150 AC: 2289 AN: 152188 Hom.: 21 Cov.: 32

Gnomad AFR AF: 0.00721

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0208

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.00575

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0196

Gnomad OTH AF: 0.0224

GnomAD3 exomes AF: 0.0161 AC: 4019 AN: 249460 Hom.: 52 AF XY: 0.0175 AC XY: 2358 AN XY: 134848

Gnomad AFR exome AF: 0.00776

Gnomad AMR exome AF: 0.0110

Gnomad ASJ exome AF: 0.0134

Gnomad EAS exome AF: 0.000163

Gnomad SAS exome AF: 0.0335

Gnomad FIN exome AF: 0.00671

Gnomad NFE exome AF: 0.0187

Gnomad OTH exome AF: 0.0184

GnomAD4 exome AF: 0.0188 AC: 26962 AN: 1437230 Hom.: 307 Cov.: 28 AF XY: 0.0193 AC XY: 13794 AN XY: 716510

Gnomad4 AFR exome AF: 0.00915

Gnomad4 AMR exome AF: 0.0113

Gnomad4 ASJ exome AF: 0.0145

Gnomad4 EAS exome AF: 0.000152

Gnomad4 SAS exome AF: 0.0350

Gnomad4 FIN exome AF: 0.00604

Gnomad4 NFE exome AF: 0.0195

Gnomad4 OTH exome AF: 0.0177

GnomAD4 genome AF: 0.0150 AC: 2292 AN: 152306 Hom.: 21 Cov.: 32 AF XY: 0.0150 AC XY: 1117 AN XY: 74480

Gnomad4 AFR AF: 0.00724

Gnomad4 AMR AF: 0.0207

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0360

Gnomad4 FIN AF: 0.00575

Gnomad4 NFE AF: 0.0196

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0169 Hom.: 8

Bravo AF: 0.0148

Asia WGS AF: 0.0140 AC: 50 AN: 3478

EpiCase AF: 0.0170

EpiControl AF: 0.0177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60069075; hg19: chr3-52729198;