rs12603456

Variant names:

• chr17-82981284-A-T
• rs12603456
• NM_001009905.3:c.460-15538T>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.460-15538T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,136 control chromosomes in the GnomAD database, including 5,769 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 0.27 (5769 hom., cov: 33)
  • Exomes 𝑓: 0.22 (0 hom.)
• Consequence: QTGAL NM_001009905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 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]

ENSG00000262339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 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.460-15538T>A		intron	N/A	NP_001009905.2	Q67FW5
	QTGAL	NM_001320742.2		c.463-15538T>A		intron	N/A	NP_001307671.1
	QTGAL	NM_001320743.2		c.-30-15538T>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.460-15538T>A		intron	N/A	ENSP00000319979.4	Q67FW5
	B3GNTL1	ENST00000905888.1		c.460-15538T>A		intron	N/A	ENSP00000575947.1
	B3GNTL1	ENST00000905890.1		c.460-15538T>A		intron	N/A	ENSP00000575949.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40929 AN: 151982 Hom.: 5768 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.222 AC: 8 AN: 36 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 8 AN XY: 32

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 6 AN: 30

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.269 AC: 40952 AN: 152100 Hom.: 5769 Cov.: 33 AF XY: 0.264 AC XY: 19606 AN XY: 74378

African (AFR) AF: 0.322 AC: 13356 AN: 41472

American (AMR) AF: 0.250 AC: 3827 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1021 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1917 AN: 5156

South Asian (SAS) AF: 0.169 AC: 815 AN: 4826

European-Finnish (FIN) AF: 0.197 AC: 2092 AN: 10596

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17021 AN: 67982

Other (OTH) AF: 0.253 AC: 532 AN: 2106

Alfa AF: 0.261 Hom.: 666

Bravo AF: 0.278

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.69
PhyloP100		0.24
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: rs12603456; hg19: chr17-80939160;