NM_001009905.3:c.460-11990G>A

Variant names:

• chr17-82977736-C-T
• rs1551628
• NM_001009905.3:c.460-11990G>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.460-11990G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,836 control chromosomes in the GnomAD database, including 19,305 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 0.50 (19305 hom., cov: 31)
• Consequence: QTGAL NM_001009905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.594 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	QTGAL	NM_001009905.3	MANE Select	c.460-11990G>A		intron	N/A	NP_001009905.2
	QTGAL	NM_001320742.2		c.463-11990G>A		intron	N/A	NP_001307671.1
	QTGAL	NM_001320743.2		c.-30-11990G>A		intron	N/A	NP_001307672.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GNTL1	ENST00000320865.4	TSL:1 MANE Select	c.460-11990G>A		intron	N/A	ENSP00000319979.4
	B3GNTL1	ENST00000576599.5	TSL:2	c.172-11990G>A		intron	N/A	ENSP00000461127.1
	B3GNTL1	ENST00000570947.5	TSL:3	n.51-30777G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75970 AN: 151720 Hom.: 19294 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.532

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.501 AC: 76028 AN: 151836 Hom.: 19305 Cov.: 31 AF XY: 0.508 AC XY: 37687 AN XY: 74214

African (AFR) AF: 0.430 AC: 17796 AN: 41384

American (AMR) AF: 0.514 AC: 7844 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1743 AN: 3470

East Asian (EAS) AF: 0.496 AC: 2542 AN: 5130

South Asian (SAS) AF: 0.613 AC: 2945 AN: 4806

European-Finnish (FIN) AF: 0.568 AC: 5991 AN: 10546

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.521 AC: 35416 AN: 67928

Other (OTH) AF: 0.537 AC: 1128 AN: 2102

Alfa AF: 0.515 Hom.: 75576

Bravo AF: 0.492

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.60
PhyloP100		-1.2
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: rs1551628; hg19: chr17-80935612;