9-127886066-G-C

Variant names:

• chr9-127886066-G-C
• rs913981
• NM_013443.5:c.*533C>G

Variant summary

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

The NM_013443.5(ST6GALNAC6):​c.*533C>G variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ST6GALNAC6 NM_013443.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.20
• Publications: 1 publications found

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

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 (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013443.5. 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
	ST6GALNAC6	NM_013443.5	MANE Select	c.*533C>G		3_prime_UTR	Exon 7 of 7	NP_038471.2
	ST6GALNAC6	NM_001286999.2		c.*406C>G		3_prime_UTR	Exon 7 of 7	NP_001273928.1	Q969X2-3
	ST6GALNAC6	NM_001400830.1		c.*533C>G		3_prime_UTR	Exon 6 of 6	NP_001387759.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC6	ENST00000373146.6	TSL:1 MANE Select	c.*533C>G		3_prime_UTR	Exon 7 of 7	ENSP00000362239.1	Q969X2-1
	ST6GALNAC6	ENST00000373142.5	TSL:1	c.*406C>G		3_prime_UTR	Exon 7 of 7	ENSP00000362235.1	Q969X2-3
	ST6GALNAC6	ENST00000373144.7	TSL:1	c.*533C>G		3_prime_UTR	Exon 6 of 6	ENSP00000362237.3	Q969X2-2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 7430 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 3756

African (AFR) AF: 0.00 AC: 0 AN: 242

American (AMR) AF: 0.00 AC: 0 AN: 436

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 298

East Asian (EAS) AF: 0.00 AC: 0 AN: 344

South Asian (SAS) AF: 0.00 AC: 0 AN: 172

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 288

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 38

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 5130

Other (OTH) AF: 0.00 AC: 0 AN: 482

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 8664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.023
DANN	Benign	0.50
PhyloP100		-4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs913981; hg19: chr9-130648345;