chr16-70398341-T-A

Variant names:

• chr16-70398341-T-A
• NM_006927.4:c.190A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006927.4(ST3GAL2):​c.190A>T​(p.Arg64Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ST3GAL2 NM_006927.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.178
• Publications: 0 publications found

Genes affected

ST3GAL2 (HGNC:10863): (ST3 beta-galactoside alpha-2,3-sialyltransferase 2) The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi but can be proteolytically processed to a soluble form. This protein, which is a member of glycosyltransferase family 29, can use the same acceptor substrates as does sialyltransferase 4A. [provided by RefSeq, Jul 2008]

ENSG00000260111 (HGNC:):

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 (MetaRNN=0.05960521).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006927.4. 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
	ST3GAL2	NM_006927.4	MANE Select	c.190A>T	p.Arg64Trp	missense	Exon 2 of 7	NP_008858.1	Q16842

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL2	ENST00000342907.3	TSL:5 MANE Select	c.190A>T	p.Arg64Trp	missense	Exon 2 of 7	ENSP00000345477.2	Q16842
	ST3GAL2	ENST00000393640.8	TSL:1	c.190A>T	p.Arg64Trp	missense	Exon 1 of 6	ENSP00000377257.4	Q16842
	ST3GAL2	ENST00000859575.1		c.190A>T	p.Arg64Trp	missense	Exon 3 of 8	ENSP00000529634.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	21
DANN	Benign	0.97
DEOGEN2	Benign	0.15	T
Eigen	Benign	-0.73
Eigen_PC	Benign	-0.61
FATHMM_MKL	Benign	0.61	D
LIST_S2	Benign	0.53	T
M_CAP	Benign	0.0093	T
MetaRNN	Benign	0.060	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		0.18
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-0.71	N
REVEL	Benign	0.059
Sift	Benign	0.19	T
Sift4G	Benign	0.18	T
Polyphen		0.044	B
Vest4		0.15
MutPred		0.38		Loss of disorder (P = 0.0045)
MVP		0.043
MPC		0.18
ClinPred		0.11	T
GERP RS		3.1
Varity_R		0.033
gMVP		0.75

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

hg19: chr16-70432244;