dbSNP rs3732443: GXYLT2:c.977-114G>A (chr3-72967433-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001080393.2(GXYLT2):c.977-114G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000155 in 645,520 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000015 ( 0 hom. )

Consequence

GXYLT2
NM_001080393.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48

Publications

0 publications found

Variant links:

Genes affected

GXYLT2 (HGNC:33383): (glucoside xylosyltransferase 2) The protein encoded by this gene is a xylosyltransferase that elongates O-linked glucose bound to epidermal growth factor (EGF) repeats. The encoded protein catalyzes the addition of xylose to the O-glucose-modified residues of EGF repeats of Notch proteins. [provided by RefSeq, Sep 2016]

GXYLT2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GXYLT2	NM_001080393.2 link	c.977-114G>A		intron_variant	Intron 5 of 6	ENST00000389617.9	NP_001073862.1	A0PJZ3
GXYLT2	NR_138564.2 link	n.1160-114G>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GXYLT2	ENST00000389617.9 link	c.977-114G>A		intron_variant	Intron 5 of 6	5	NM_001080393.2	ENSP00000374268.4		A0PJZ3
GXYLT2	ENST00000491839.1 link	c.260-114G>A		intron_variant	Intron 2 of 3	3		ENSP00000420426.1		C9JND4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000155

AC:

AN:

645520

Hom.:

AF XY:

0.00000303

AC XY:

AN XY:

329752

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

15922

American (AMR)

AF:

0.00

AC:

AN:

19140

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14550

East Asian (EAS)

AF:

0.00

AC:

AN:

30784

South Asian (SAS)

AF:

0.0000213

AC:

AN:

47036

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35026

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2314

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

448844

Other (OTH)

AF:

0.00

AC:

AN:

31904

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.056

(source)

DANN

Benign

0.73

PhyloP100

-2.5

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over