chr3-72967433-G-A

Variant names:

• chr3-72967433-G-A
• rs3732443
• NM_001080393.2:c.977-114G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 0 publications found

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]

ACMG classification

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080393.2. 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
	GXYLT2	NM_001080393.2	MANE Select	c.977-114G>A		intron	N/A	NP_001073862.1
	GXYLT2	NR_138564.2		n.1160-114G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GXYLT2	ENST00000389617.9	TSL:5 MANE Select	c.977-114G>A		intron	N/A	ENSP00000374268.4
	GXYLT2	ENST00000491839.1	TSL:3	c.260-114G>A		intron	N/A	ENSP00000420426.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000155 AC: 1 AN: 645520 Hom.: 0 AF XY: 0.00000303 AC XY: 1 AN XY: 329752

African (AFR) AF: 0.00 AC: 0 AN: 15922

American (AMR) AF: 0.00 AC: 0 AN: 19140

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14550

East Asian (EAS) AF: 0.00 AC: 0 AN: 30784

South Asian (SAS) AF: 0.0000213 AC: 1 AN: 47036

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35026

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 448844

Other (OTH) AF: 0.00 AC: 0 AN: 31904

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.056
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

Other links and lift over

dbSNP: rs3732443; hg19: chr3-73016584;