Genetic Variant ST8SIA6:c.201-7776T>C (chr10-17398396-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001004470.3(ST8SIA6):c.201-7776T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0325 in 152,230 control chromosomes in the GnomAD database, including 84 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 0.033 ( 84 hom., cov: 32)

Consequence

ST8SIA6
NM_001004470.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.523

Publications

1 publications found

Variant links:

Genes affected

ST8SIA6 (HGNC:23317): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6) This gene encodes a member of the glycosyltransferase 29 protein family. Members of this protein family synthesize sialylglycoconjugates. Sialylation may contribute to multidrug resistance in cancer cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ST8SIA6 links:

ST8SIA6-AS1 (HGNC:44880): (ST8SIA6 antisense RNA 1)

ST8SIA6-AS1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001004470.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004470.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ST8SIA6	NM_001004470.3	MANE Select	c.201-7776T>C	intron	N/A	NP_001004470.1	P61647
ST8SIA6	NM_001345961.2		c.-322-7776T>C	intron	N/A	NP_001332890.1
ST8SIA6-AS1	NR_034129.1		n.141-709A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ST8SIA6	ENST00000377602.5	TSL:1 MANE Select	c.201-7776T>C	intron	N/A	ENSP00000366827.4	P61647
ST8SIA6-AS1	ENST00000457649.7	TSL:1	n.165-709A>G	intron	N/A
ST8SIA6-AS1	ENST00000377597.6	TSL:2	n.126-709A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0324

AC:

4936

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0425

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0305

Gnomad ASJ

AF:

0.0199

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0550

Gnomad FIN

AF:

0.0190

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0308

Gnomad OTH

AF:

0.0292

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0325

AC:

4949

AN:

152230

Hom.:

Cov.:

AF XY:

0.0318

AC XY:

2363

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0426

AC:

1771

AN:

41552

American (AMR)

AF:

0.0306

AC:

468

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0199

AC:

AN:

3470

East Asian (EAS)

AF:

0.00155

AC:

AN:

5172

South Asian (SAS)

AF:

0.0555

AC:

268

AN:

4828

European-Finnish (FIN)

AF:

0.0190

AC:

202

AN:

10610

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0308

AC:

2094

AN:

68006

Other (OTH)

AF:

0.0289

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

230

461

691

922

1152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0348

Hom.:

Bravo

AF:

0.0329

Asia WGS

AF:

0.0320

AC:

110

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.12

(source)

DANN

Benign

0.61

PhyloP100

-0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over