17-82946964-A-T

Variant names:

• chr17-82946964-A-T
• rs752672514
• NM_001009905.3:c.980T>A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001009905.3(QTGAL):​c.980T>A​(p.Phe327Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000707 in 1,414,932 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F327S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: QTGAL NM_001009905.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.23
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.980T>A	p.Phe327Tyr	missense	Exon 12 of 13	NP_001009905.2	Q67FW5
	QTGAL	NM_001320742.2		c.983T>A	p.Phe328Tyr	missense	Exon 13 of 14	NP_001307671.1
	QTGAL	NM_001320743.2		c.491T>A	p.Phe164Tyr	missense	Exon 8 of 9	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.980T>A	p.Phe327Tyr	missense	Exon 12 of 13	ENSP00000319979.4	Q67FW5
	B3GNTL1	ENST00000571301.1	TSL:1	n.2985T>A		non_coding_transcript_exon	Exon 1 of 2
	B3GNTL1	ENST00000905888.1		c.980T>A	p.Phe327Tyr	missense	Exon 12 of 13	ENSP00000575947.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.07e-7 AC: 1 AN: 1414932 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 699266

African (AFR) AF: 0.0000308 AC: 1 AN: 32476

American (AMR) AF: 0.00 AC: 0 AN: 38026

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25272

East Asian (EAS) AF: 0.00 AC: 0 AN: 37288

South Asian (SAS) AF: 0.00 AC: 0 AN: 80220

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50260

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5712

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1087044

Other (OTH) AF: 0.00 AC: 0 AN: 58634

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.64
BayesDel_addAF	Benign	-0.011	T
BayesDel_noAF	Benign	-0.25
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.097	T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Benign	0.76	D
LIST_S2	Benign	0.85	D
M_CAP	Benign	0.012	T
MetaRNN	Uncertain	0.57	D
MetaSVM	Uncertain	-0.21	T
MutationAssessor	Uncertain	2.7	M
PhyloP100		4.2
PrimateAI	Uncertain	0.69	T
PROVEAN	Uncertain	-2.4	N
REVEL	Benign	0.20
Sift	Uncertain	0.016	D
Sift4G	Uncertain	0.020	D
Polyphen		1.0	D
Vest4		0.65
MutPred		0.34		Gain of loop (P = 0.0097)
MVP		0.58
MPC		0.54
ClinPred		0.95	D
GERP RS		4.0
Varity_R		0.33
gMVP		0.40
Mutation Taster		=86/14	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: rs752672514; hg19: chr17-80904840;