NM_173601.2:c.865-3291C>T

Variant names:

• chr12-42101324-G-A
• rs6582380
• NM_173601.2:c.865-3291C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_173601.2(GXYLT1):​c.865-3291C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00457 in 152,066 control chromosomes in the GnomAD database, including 8 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 0.0046 (8 hom., cov: 32)
• Consequence: GXYLT1 NM_173601.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00457 (695/152066) while in subpopulation AFR AF = 0.0164 (679/41494). AF 95% confidence interval is 0.0153. There are 8 homozygotes in GnomAd4. There are 337 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GXYLT1	NM_173601.2	c.865-3291C>T		intron_variant	Intron 5 of 7	ENST00000398675.8	NP_775872.1
GXYLT1	NM_001099650.2	c.772-3291C>T		intron_variant	Intron 4 of 6		NP_001093120.1
GXYLT1	XM_017019211.1	c.520-3291C>T		intron_variant	Intron 5 of 7		XP_016874700.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GXYLT1	ENST00000398675.8	c.865-3291C>T		intron_variant	Intron 5 of 7	1	NM_173601.2	ENSP00000381666.3
GXYLT1	ENST00000280876.6	c.772-3291C>T		intron_variant	Intron 4 of 6	1		ENSP00000280876.6

Frequencies

GnomAD3 genomes AF: 0.00457 AC: 694 AN: 151950 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.0164

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000590

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00144

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00457 AC: 695 AN: 152066 Hom.: 8 Cov.: 32 AF XY: 0.00453 AC XY: 337 AN XY: 74342

African (AFR) AF: 0.0164 AC: 679 AN: 41494

American (AMR) AF: 0.000589 AC: 9 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10530

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 67982

Other (OTH) AF: 0.00143 AC: 3 AN: 2104

Alfa AF: 0.00573 Hom.: 1

Bravo AF: 0.00539

Asia WGS AF: 0.00260 AC: 9 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.62
PhyloP100		0.061
Mutation Taster		=100/0	polymorphism

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: rs6582380; hg19: chr12-42495126;