Variant rs10064618 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT10	NM_198321.4 link	c.1056+6299G>A		intron_variant		ENST00000297107.11	NP_938080.1	Q86SR1-1
SAP30L-AS1	NR_037897.1 link	n.490C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT10	ENST00000297107.11 link	c.1056+6299G>A		intron_variant		1	NM_198321.4	ENSP00000297107.6		Q86SR1-1

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

Gnomad4 AFR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.438

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.523

AC:

79443

AN:

151854

Hom.:

22354

Cov.:

AF XY:

0.528

AC XY:

39172

AN XY:

74180

show subpopulations

Gnomad4 AFR

AF:

0.719

Gnomad4 AMR

AF:

0.537

Gnomad4 ASJ

AF:

0.408

Gnomad4 EAS

AF:

0.649

Gnomad4 SAS

AF:

0.529

Gnomad4 FIN

AF:

0.513

Gnomad4 NFE

AF:

0.398

Gnomad4 OTH

AF:

0.509

Alfa

AF:

0.423

Hom.:

20579

Bravo

AF:

0.537

Asia WGS

AF:

0.617

AC:

2143

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.8

DANN

Benign

0.47

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over