12-42109700-AT-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_173601.2(GXYLT1):c.487-10del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00083 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: GXYLT1 NM_173601.2 splice_polypyrimidine_tract, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.564

Genes affected

GXYLT1 (HGNC:27482): (glucoside xylosyltransferase 1) GXYLT1 is a xylosyltransferase (EC 2.4.2.-) that adds the first xylose to O-glucose-modified residues in the epidermal growth factor (EGF; MIM 131530) repeats of proteins such as NOTCH1 (MIM 190198) (Sethi et al., 2010 [PubMed 19940119]).[supplied by OMIM, Mar 2010]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 12-42109700-AT-A is Benign according to our data. Variant chr12-42109700-AT-A is described in ClinVar as [Likely_benign]. Clinvar id is 2723349.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GXYLT1	NM_173601.2	c.487-10del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000398675.8
GXYLT1	NM_001099650.2	c.394-10del		splice_polypyrimidine_tract_variant, intron_variant
GXYLT1	XM_017019211.1	c.142-10del		splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GXYLT1	ENST00000398675.8	c.487-10del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_173601.2	P4
GXYLT1	ENST00000280876.6	c.394-10del		splice_polypyrimidine_tract_variant, intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2 AN: 148240 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000999

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000835 AC: 1056 AN: 1264888 Hom.: 1 Cov.: 20 AF XY: 0.000780 AC XY: 495 AN XY: 634438

Gnomad4 AFR exome AF: 0.00119

Gnomad4 AMR exome AF: 0.00176

Gnomad4 ASJ exome AF: 0.000727

Gnomad4 EAS exome AF: 0.000810

Gnomad4 SAS exome AF: 0.00127

Gnomad4 FIN exome AF: 0.000214

Gnomad4 NFE exome AF: 0.000778

Gnomad4 OTH exome AF: 0.00100

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000135 AC: 2 AN: 148240 Hom.: 0 Cov.: 32 AF XY: 0.0000277 AC XY: 2 AN XY: 72238

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000999

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00495 Hom.: 9

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 28, 2023

- -

Computational scores

Source: dbNSFP v4.3

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

LitVar

Other links and lift over

dbSNP: rs111700961; hg19: chr12-42503502;