17-83005455-C-T

Variant names:

• chr17-83005455-C-T
• rs9901757
• NM_001009905.3:c.364-245G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009905.3(QTGAL):​c.364-245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 629,114 control chromosomes in the GnomAD database, including 95,029 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.52 (20977 hom., cov: 31)
  • Exomes 𝑓: 0.56 (74052 hom.)
• Consequence: QTGAL NM_001009905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 23 publications found

Genes affected

QTGAL (HGNC:21727): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1) Predicted to enable glycosyltransferase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001009905.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QTGAL	NM_001009905.3	MANE Select	c.364-245G>A		intron	N/A	NP_001009905.2	Q67FW5
	QTGAL	NM_001320742.2		c.367-245G>A		intron	N/A	NP_001307671.1
	QTGAL	NM_001320743.2		c.-126-245G>A		intron	N/A	NP_001307672.1	I3L232

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GNTL1	ENST00000320865.4	TSL:1 MANE Select	c.364-245G>A		intron	N/A	ENSP00000319979.4	Q67FW5
	B3GNTL1	ENST00000905888.1		c.364-245G>A		intron	N/A	ENSP00000575947.1
	B3GNTL1	ENST00000905890.1		c.364-245G>A		intron	N/A	ENSP00000575949.1

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79181 AN: 151808 Hom.: 20974 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.526

GnomAD4 exome AF: 0.555 AC: 264850 AN: 477188 Hom.: 74052 AF XY: 0.558 AC XY: 140258 AN XY: 251468

African (AFR) AF: 0.445 AC: 6255 AN: 14050

American (AMR) AF: 0.540 AC: 15156 AN: 28082

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 9298 AN: 15848

East Asian (EAS) AF: 0.520 AC: 16089 AN: 30918

South Asian (SAS) AF: 0.597 AC: 29807 AN: 49890

European-Finnish (FIN) AF: 0.539 AC: 16754 AN: 31090

Middle Eastern (MID) AF: 0.628 AC: 2166 AN: 3448

European-Non Finnish (NFE) AF: 0.558 AC: 154239 AN: 276414

Other (OTH) AF: 0.550 AC: 15086 AN: 27448

GnomAD4 genome AF: 0.521 AC: 79214 AN: 151926 Hom.: 20977 Cov.: 31 AF XY: 0.522 AC XY: 38728 AN XY: 74256

African (AFR) AF: 0.446 AC: 18474 AN: 41410

American (AMR) AF: 0.528 AC: 8065 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2071 AN: 3466

East Asian (EAS) AF: 0.483 AC: 2494 AN: 5164

South Asian (SAS) AF: 0.596 AC: 2872 AN: 4822

European-Finnish (FIN) AF: 0.535 AC: 5644 AN: 10546

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37881 AN: 67938

Other (OTH) AF: 0.520 AC: 1095 AN: 2106

Alfa AF: 0.544 Hom.: 89912

Bravo AF: 0.515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.61
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9901757; hg19: chr17-80963331; COSMIC: COSV57948942;