rs113218677

Variant names:

• chr1-33307191-C-A
• rs113218677
• NM_001080438.1:c.598G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-33307191-C-A
• chr1-33307191-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001080438.1(A3GALT2):​c.598G>T​(p.Val200Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000359 in 1,392,232 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V200M) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000036 (0 hom.)
• Consequence: A3GALT2 NM_001080438.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932
• Publications: 0 publications found

Genes affected

A3GALT2 (HGNC:30005): (alpha 1,3-galactosyltransferase 2) Predicted to enable N-acetyllactosaminide 3-alpha-galactosyltransferase activity and alpha-1,3-galactosyltransferase activity. Predicted to be involved in lipid glycosylation. Predicted to act upstream of or within glycosphingolipid biosynthetic process. Predicted to be located in Golgi cisterna membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus and vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000225313 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.32011595).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080438.1. 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
	A3GALT2	NM_001080438.1	MANE Select	c.598G>T	p.Val200Leu	missense	Exon 5 of 5	NP_001073907.1	U3KPV4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	A3GALT2	ENST00000442999.3	TSL:5 MANE Select	c.598G>T	p.Val200Leu	missense	Exon 5 of 5	ENSP00000475261.1	U3KPV4
	ENSG00000225313	ENST00000457957.2	TSL:5	n.-180C>A		upstream_gene	N/A
	ENSG00000225313	ENST00000588828.1	TSL:5	n.-175C>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000359 AC: 5 AN: 1392232 Hom.: 0 Cov.: 32 AF XY: 0.00000290 AC XY: 2 AN XY: 688764

African (AFR) AF: 0.00 AC: 0 AN: 29076

American (AMR) AF: 0.00 AC: 0 AN: 36118

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24550

East Asian (EAS) AF: 0.00 AC: 0 AN: 33580

South Asian (SAS) AF: 0.00 AC: 0 AN: 77970

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5646

European-Non Finnish (NFE) AF: 0.00000463 AC: 5 AN: 1080922

Other (OTH) AF: 0.00 AC: 0 AN: 57758

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.34
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.040
CADD	Uncertain	23
DANN	Benign	0.78
DEOGEN2	Benign	0.24	T
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Benign	0.77	T
M_CAP	Uncertain	0.26	D
MetaRNN	Benign	0.32	T
PhyloP100		0.93
PrimateAI	Uncertain	0.68	T
Sift4G	Uncertain	0.0080	D
Vest4		0.42
MVP		0.36
MPC		0.53
GERP RS		2.5
Varity_R		0.068
gMVP		0.72
Mutation Taster		=92/8	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: rs113218677; hg19: chr1-33772792;