rs9901757

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-83005455-C-A
• chr17-83005455-C-G
• chr17-83005455-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001009905.3(QTGAL):​c.364-245G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000126 in 477,540 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.000013 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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>T		intron	N/A	NP_001009905.2	Q67FW5
	QTGAL	NM_001320742.2		c.367-245G>T		intron	N/A	NP_001307671.1
	QTGAL	NM_001320743.2		c.-126-245G>T		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>T		intron	N/A	ENSP00000319979.4	Q67FW5
	B3GNTL1	ENST00000905888.1		c.364-245G>T		intron	N/A	ENSP00000575947.1
	B3GNTL1	ENST00000905890.1		c.364-245G>T		intron	N/A	ENSP00000575949.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.0000126 AC: 6 AN: 477540 Hom.: 0 AF XY: 0.0000238 AC XY: 6 AN XY: 251664

African (AFR) AF: 0.00 AC: 0 AN: 14068

American (AMR) AF: 0.00 AC: 0 AN: 28134

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15862

East Asian (EAS) AF: 0.00 AC: 0 AN: 30936

South Asian (SAS) AF: 0.000120 AC: 6 AN: 49950

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31108

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3454

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 276574

Other (OTH) AF: 0.00 AC: 0 AN: 27454

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.52
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

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;