dbSNP rs10064618: GALNT10:c.1056+6299G>A (chr5-154392729-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_198321.4(GALNT10):c.1056+6299G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,876 control chromosomes in the GnomAD database, including 22,357 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 0.52 ( 22354 hom., cov: 31)

Exomes 𝑓: 0.45 ( 3 hom. )

Consequence

GALNT10
NM_198321.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.109

Publications

5 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:

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

SAP30L-AS1 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

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.1056+6299G>A		intron	N/A	NP_938080.1	Q86SR1-1
	SAP30L-AS1	NR_037897.1		n.490C>T		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GALNT10	ENST00000297107.11	TSL:1 MANE Select	c.1056+6299G>A	intron	N/A	ENSP00000297107.6	Q86SR1-1
SAP30L-AS1	ENST00000524264.6	TSL:1	n.481C>T	non_coding_transcript_exon	Exon 3 of 3
GALNT10	ENST00000969502.1		c.1057-536G>A	intron	N/A	ENSP00000639561.1

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79337

AN:

151736

Hom.:

22309

Cov.:

show subpopulations

Gnomad AFR

AF:

0.719

Gnomad AMI

AF:

0.587

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.408

Gnomad EAS

AF:

0.650

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.513

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.511

GnomAD4 exome

AF:

0.455

AC:

AN:

Hom.:

Cov.:

AF XY:

0.455

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.438

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.713

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.523

AC:

79443

AN:

151854

Hom.:

22354

Cov.:

AF XY:

0.528

AC XY:

39172

AN XY:

74180

show subpopulations

African (AFR)

AF:

0.719

AC:

29763

AN:

41396

American (AMR)

AF:

0.537

AC:

8199

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.408

AC:

1416

AN:

3468

East Asian (EAS)

AF:

0.649

AC:

3344

AN:

5150

South Asian (SAS)

AF:

0.529

AC:

2551

AN:

4824

European-Finnish (FIN)

AF:

0.513

AC:

5373

AN:

10482

Middle Eastern (MID)

AF:

0.425

AC:

124

AN:

292

European-Non Finnish (NFE)

AF:

0.398

AC:

27061

AN:

67942

Other (OTH)

AF:

0.509

AC:

1077

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1797

3595

5392

7190

8987

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

676

1352

2028

2704

3380

<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:

0.432

Hom.:

29649

Bravo

AF:

0.537

Asia WGS

AF:

0.617

AC:

2143

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.8

(source)

DANN

Benign

0.47

PhyloP100

-0.11

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

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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