17-82956724-G-T

Variant names:

• chr17-82956724-G-T
• rs57857201
• NM_001009905.3:c.931C>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001009905.3(QTGAL):​c.931C>A​(p.Arg311Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00581 in 1,589,534 control chromosomes in the GnomAD database, including 431 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 0.030 (222 hom., cov: 33)
  • Exomes 𝑓: 0.0032 (209 hom.)
• Consequence: QTGAL NM_001009905.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427
• Publications: 4 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP7: Synonymous conserved (PhyloP=0.427 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 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.931C>A	p.Arg311Arg	synonymous	Exon 11 of 13	NP_001009905.2	Q67FW5
	QTGAL	NM_001320742.2		c.934C>A	p.Arg312Arg	synonymous	Exon 12 of 14	NP_001307671.1
	QTGAL	NM_001320743.2		c.442C>A	p.Arg148Arg	synonymous	Exon 7 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.931C>A	p.Arg311Arg	synonymous	Exon 11 of 13	ENSP00000319979.4	Q67FW5
	B3GNTL1	ENST00000905888.1		c.931C>A	p.Arg311Arg	synonymous	Exon 11 of 13	ENSP00000575947.1
	B3GNTL1	ENST00000905890.1		c.931C>A	p.Arg311Arg	synonymous	Exon 11 of 13	ENSP00000575949.1

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4571 AN: 152234 Hom.: 219 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000676

Gnomad OTH AF: 0.0277

GnomAD2 exomes AF: 0.00693 AC: 1463 AN: 211038 AF XY: 0.00530

Gnomad AFR exome AF: 0.0976

Gnomad AMR exome AF: 0.00572

Gnomad ASJ exome AF: 0.000648

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000528

Gnomad OTH exome AF: 0.00470

GnomAD4 exome AF: 0.00324 AC: 4652 AN: 1437182 Hom.: 209 Cov.: 31 AF XY: 0.00287 AC XY: 2047 AN XY: 712628

African (AFR) AF: 0.106 AC: 3474 AN: 32862

American (AMR) AF: 0.00686 AC: 283 AN: 41228

Ashkenazi Jewish (ASJ) AF: 0.000741 AC: 19 AN: 25644

East Asian (EAS) AF: 0.00 AC: 0 AN: 38268

South Asian (SAS) AF: 0.000207 AC: 17 AN: 82218

European-Finnish (FIN) AF: 0.0000194 AC: 1 AN: 51638

Middle Eastern (MID) AF: 0.0110 AC: 63 AN: 5738

European-Non Finnish (NFE) AF: 0.000301 AC: 331 AN: 1100164

Other (OTH) AF: 0.00781 AC: 464 AN: 59422

GnomAD4 genome AF: 0.0301 AC: 4583 AN: 152352 Hom.: 222 Cov.: 33 AF XY: 0.0289 AC XY: 2151 AN XY: 74500

African (AFR) AF: 0.103 AC: 4287 AN: 41576

American (AMR) AF: 0.0118 AC: 181 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.000676 AC: 46 AN: 68034

Other (OTH) AF: 0.0274 AC: 58 AN: 2116

Alfa AF: 0.00952 Hom.: 32

Bravo AF: 0.0338

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.4
DANN	Benign	0.51
PhyloP100		0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs57857201; hg19: chr17-80914600; COSMIC: COSV100302025; COSMIC: COSV100302025;