dbSNP rs12603456: QTGAL:c.460-15538T>A (chr17-82981284-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

1 publications found

Variant links:

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]

QTGAL links:

ENSG00000262339 (HGNC:):

ENSG00000262339 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
QTGAL	NM_001009905.3 link	c.460-15538T>A		intron_variant	Intron 6 of 12	ENST00000320865.4	NP_001009905.2	Q67FW5A0A024R8X6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GNTL1	ENST00000320865.4 link	c.460-15538T>A		intron_variant	Intron 6 of 12	1	NM_001009905.3	ENSP00000319979.4		Q67FW5

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40929

AN:

151982

Hom.:

5768

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.200

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.444

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.269

AC:

40952

AN:

152100

Hom.:

5769

Cov.:

AF XY:

0.264

AC XY:

19606

AN XY:

74378

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

17021

AN:

67982

Other (OTH)

AF:

0.253

AC:

532

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1523

3046

4570

6093

7616

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.7

(source)

DANN

Benign

0.69

PhyloP100

0.24

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over