rs779584534

Variant names:

• chr9-127894670-C-A
• rs779584534
• NM_013443.5:c.139G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-127894670-C-A
• chr9-127894670-C-G
• chr9-127894670-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_013443.5(ST6GALNAC6):​c.139G>T​(p.Val47Leu) 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. 14/21 in silico tools predict 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. V47M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ST6GALNAC6 NM_013443.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.97

Genes affected

ST6GALNAC6 (HGNC:23364): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6) ST6GALNAC6 belongs to a family of sialyltransferases that modify proteins and ceramides on the cell surface to alter cell-cell or cell-extracellular matrix interactions (Tsuchida et al., 2003 [PubMed 12668675]).[supplied by OMIM, Mar 2008]

ENSG00000257524 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.111803025).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC6	NM_013443.5	c.139G>T	p.Val47Leu	missense_variant	Exon 4 of 7	ENST00000373146.6	NP_038471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC6	ENST00000373146.6	c.139G>T	p.Val47Leu	missense_variant	Exon 4 of 7	1	NM_013443.5	ENSP00000362239.1
ENSG00000257524	ENST00000646171.1	n.37G>T		non_coding_transcript_exon_variant	Exon 3 of 13			ENSP00000495484.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	20
DANN	Benign	0.96
DEOGEN2	Benign	0.030	.;T;T;.;.;.;.;.
Eigen	Benign	-0.55
Eigen_PC	Benign	-0.34
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.80	T;T;.;T;.;T;.;T
M_CAP	Benign	0.0058	T
MetaRNN	Benign	0.11	T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.55	.;N;N;.;.;N;.;.
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-0.29	.;N;N;.;N;N;N;N
REVEL	Benign	0.052
Sift	Benign	0.22	.;T;T;.;T;D;T;T
Sift4G	Benign	0.35	T;T;T;T;T;T;T;.
Polyphen		0.035, 0.018	.;B;B;B;B;.;B;.
Vest4		0.31
MutPred		0.50		.;Gain of helix (P = 0.0022);Gain of helix (P = 0.0022);.;.;Gain of helix (P = 0.0022);.;.;
MVP		0.26
MPC		0.46
ClinPred		0.16	T
GERP RS		3.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.031
gMVP		0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs779584534; hg19: chr9-130656949;