rs13186787

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_198321.4(GALNT10):c.568+17471A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 479,186 control chromosomes in the GnomAD database, including 118 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 0.014 ( 26 hom., cov: 29)

Exomes 𝑓: 0.021 ( 92 hom. )

Consequence

GALNT10
NM_198321.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.803

Publications

11 publications found

Variant links:

Genes affected

GALNT10 (HGNC:19873): (polypeptide N-acetylgalactosaminyltransferase 10) This gene encodes a member of the GalNAc polypeptide N-acetylgalactosaminyltransferases. These enzymes catalyze the first step in the synthesis of mucin-type oligosaccharides. These proteins transfer GalNAc from UDP-GalNAc to either serine or threonine residues of polypeptide acceptors. The protein encoded by this locus may have increased catalytic activity toward glycosylated peptides compared to activity toward non-glycosylated peptides.[provided by RefSeq, Apr 2010]

GALNT10 links:

MIR1294 (HGNC:35287): (microRNA 1294) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR1294 links:

SAP30L-AS1 (HGNC:26760): (SAP30L antisense RNA 1 (head to head))

SAP30L-AS1 links:

ENSG00000287695 (HGNC:):

ENSG00000287695 links:

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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=-0.95).

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0144 (2146/149032) while in subpopulation SAS AF = 0.0308 (138/4484). AF 95% confidence interval is 0.0266. There are 26 homozygotes in GnomAd4. There are 990 alleles in the male GnomAd4 subpopulation. Median coverage is 29. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 26 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198321.4. 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
	GALNT10	NM_198321.4	MANE Select	c.568+17471A>G		intron	N/A	NP_938080.1	Q86SR1-1
	MIR1294	NR_031626.1		n.104A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GALNT10	ENST00000297107.11	TSL:1 MANE Select	c.568+17471A>G	intron	N/A	ENSP00000297107.6	Q86SR1-1
GALNT10	ENST00000969502.1		c.568+17471A>G	intron	N/A	ENSP00000639561.1
GALNT10	ENST00000917832.1		c.568+17471A>G	intron	N/A	ENSP00000587891.1

Frequencies

GnomAD3 genomes

AF:

0.0144

AC:

2147

AN:

148908

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00374

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0111

Gnomad ASJ

AF:

0.00639

Gnomad EAS

AF:

0.000211

Gnomad SAS

AF:

0.0305

Gnomad FIN

AF:

0.0102

Gnomad MID

AF:

0.0382

Gnomad NFE

AF:

0.0228

Gnomad OTH

AF:

0.0117

GnomAD2 exomes

AF:

0.0187

AC:

3623

AN:

193712

AF XY:

0.0201

show subpopulations

Gnomad AFR exome

AF:

0.00393

Gnomad AMR exome

AF:

0.00972

Gnomad ASJ exome

AF:

0.00992

Gnomad EAS exome

AF:

0.0000850

Gnomad FIN exome

AF:

0.0122

Gnomad NFE exome

AF:

0.0239

Gnomad OTH exome

AF:

0.0215

GnomAD4 exome

AF:

0.0208

AC:

6864

AN:

330154

Hom.:

Cov.:

AF XY:

0.0219

AC XY:

4182

AN XY:

191212

show subpopulations

African (AFR)

AF:

0.00379

AC:

AN:

6868

American (AMR)

AF:

0.00887

AC:

185

AN:

20850

Ashkenazi Jewish (ASJ)

AF:

0.00973

AC:

AN:

9558

East Asian (EAS)

AF:

0.00

AC:

AN:

9230

South Asian (SAS)

AF:

0.0306

AC:

1761

AN:

57614

European-Finnish (FIN)

AF:

0.0129

AC:

408

AN:

31620

Middle Eastern (MID)

AF:

0.0169

AC:

AN:

2726

European-Non Finnish (NFE)

AF:

0.0228

AC:

4038

AN:

177306

Other (OTH)

AF:

0.0213

AC:

307

AN:

14382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

333

665

998

1330

1663

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0144

AC:

2146

AN:

149032

Hom.:

Cov.:

AF XY:

0.0136

AC XY:

990

AN XY:

72854

show subpopulations

African (AFR)

AF:

0.00373

AC:

152

AN:

40792

American (AMR)

AF:

0.0110

AC:

167

AN:

15124

Ashkenazi Jewish (ASJ)

AF:

0.00639

AC:

AN:

3442

East Asian (EAS)

AF:

0.000212

AC:

AN:

4726

South Asian (SAS)

AF:

0.0308

AC:

138

AN:

4484

European-Finnish (FIN)

AF:

0.0102

AC:

105

AN:

10306

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0228

AC:

1526

AN:

66888

Other (OTH)

AF:

0.0111

AC:

AN:

2074

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.549

Heterozygous variant carriers

101

203

304

406

507

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.0173

Hom.:

Bravo

AF:

0.0135

Asia WGS

AF:

0.00577

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.3

(source)

DANN

Benign

0.31

PhyloP100

-0.80

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over