rs3734083

Variant names:

• chr5-154385679-T-C
• rs3734083
• NM_198321.4:c.939-634T>C

Variant summary

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

The NM_198321.4(GALNT10):​c.939-634T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,142 control chromosomes in the GnomAD database, including 43,481 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 0.75 (43481 hom., cov: 32)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705
• Publications: 5 publications found

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]

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT10	NM_198321.4	c.939-634T>C		intron_variant	Intron 6 of 11	ENST00000297107.11	NP_938080.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT10	ENST00000297107.11	c.939-634T>C		intron_variant	Intron 6 of 11	1	NM_198321.4	ENSP00000297107.6

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114767 AN: 152024 Hom.: 43447 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.755 AC: 114858 AN: 152142 Hom.: 43481 Cov.: 32 AF XY: 0.751 AC XY: 55865 AN XY: 74366

African (AFR) AF: 0.820 AC: 34055 AN: 41518

American (AMR) AF: 0.773 AC: 11806 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2543 AN: 3470

East Asian (EAS) AF: 0.773 AC: 3991 AN: 5164

South Asian (SAS) AF: 0.650 AC: 3130 AN: 4816

European-Finnish (FIN) AF: 0.708 AC: 7496 AN: 10582

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49309 AN: 67996

Other (OTH) AF: 0.753 AC: 1590 AN: 2112

Alfa AF: 0.729 Hom.: 22682

Bravo AF: 0.769

Asia WGS AF: 0.735 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.48
PhyloP100		-0.70
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: rs3734083; hg19: chr5-153765239;