rs913981

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-127886066-G-A
• chr9-127886066-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013443.5(ST6GALNAC6):​c.*533C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.981 in 159,656 control chromosomes in the GnomAD database, including 76,866 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 0.98 (73171 hom., cov: 30)
  • Exomes 𝑓: 1.0 (3695 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC6	NM_013443.5	c.*533C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000373146.6	NP_038471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC6	ENST00000373146.6	c.*533C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_013443.5	ENSP00000362239.1
ENSG00000257524	ENST00000646171.1	n.863+570C>T		intron_variant	Intron 6 of 12			ENSP00000495484.1

Frequencies

GnomAD3 genomes AF: 0.980 AC: 149066 AN: 152108 Hom.: 73117 Cov.: 30

Gnomad AFR AF: 0.931

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.990

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.984

GnomAD4 exome AF: 0.997 AC: 7410 AN: 7430 Hom.: 3695 Cov.: 0 AF XY: 0.998 AC XY: 3747 AN XY: 3756

African (AFR) AF: 0.942 AC: 228 AN: 242

American (AMR) AF: 0.991 AC: 432 AN: 436

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 298 AN: 298

East Asian (EAS) AF: 1.00 AC: 344 AN: 344

South Asian (SAS) AF: 1.00 AC: 172 AN: 172

European-Finnish (FIN) AF: 1.00 AC: 288 AN: 288

Middle Eastern (MID) AF: 1.00 AC: 38 AN: 38

European-Non Finnish (NFE) AF: 1.00 AC: 5130 AN: 5130

Other (OTH) AF: 0.996 AC: 480 AN: 482

GnomAD4 genome AF: 0.980 AC: 149179 AN: 152226 Hom.: 73171 Cov.: 30 AF XY: 0.981 AC XY: 72987 AN XY: 74428

African (AFR) AF: 0.931 AC: 38686 AN: 41540

American (AMR) AF: 0.991 AC: 15143 AN: 15288

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5160 AN: 5160

South Asian (SAS) AF: 1.00 AC: 4826 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10616 AN: 10616

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67995 AN: 68006

Other (OTH) AF: 0.984 AC: 2078 AN: 2112

Alfa AF: 0.989 Hom.: 8664

Bravo AF: 0.977

Asia WGS AF: 0.994 AC: 3456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.029
DANN	Benign	0.45
PhyloP100		-4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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;