5-154404193-C-T

Variant names:

• chr5-154404193-C-T
• rs6580076
• NM_198321.4:c.1146C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_198321.4(GALNT10):​c.1146C>T​(p.Ala382Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,600,216 control chromosomes in the GnomAD database, including 33,545 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 0.25 (6016 hom., cov: 32)
  • Exomes 𝑓: 0.18 (27529 hom.)
• Consequence: GALNT10 NM_198321.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 18 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BP7: Synonymous conserved (PhyloP=-2.44 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT10	NM_198321.4	c.1146C>T	p.Ala382Ala	synonymous_variant	Exon 8 of 12	ENST00000297107.11	NP_938080.1
SAP30L-AS1	NR_037897.1	n.205-11179G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT10	ENST00000297107.11	c.1146C>T	p.Ala382Ala	synonymous_variant	Exon 8 of 12	1	NM_198321.4	ENSP00000297107.6

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37877 AN: 151994 Hom.: 5998 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.233

GnomAD2 exomes AF: 0.205 AC: 48889 AN: 238802 AF XY: 0.210

Gnomad AFR exome AF: 0.446

Gnomad AMR exome AF: 0.132

Gnomad ASJ exome AF: 0.194

Gnomad EAS exome AF: 0.177

Gnomad FIN exome AF: 0.152

Gnomad NFE exome AF: 0.169

Gnomad OTH exome AF: 0.191

GnomAD4 exome AF: 0.184 AC: 266675 AN: 1448104 Hom.: 27529 Cov.: 30 AF XY: 0.188 AC XY: 135448 AN XY: 719492

African (AFR) AF: 0.449 AC: 14955 AN: 33308

American (AMR) AF: 0.135 AC: 5916 AN: 43936

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 4685 AN: 25036

East Asian (EAS) AF: 0.166 AC: 6573 AN: 39576

South Asian (SAS) AF: 0.340 AC: 28715 AN: 84530

European-Finnish (FIN) AF: 0.149 AC: 7881 AN: 52872

Middle Eastern (MID) AF: 0.236 AC: 1342 AN: 5692

European-Non Finnish (NFE) AF: 0.167 AC: 184451 AN: 1103318

Other (OTH) AF: 0.203 AC: 12157 AN: 59836

GnomAD4 genome AF: 0.249 AC: 37934 AN: 152112 Hom.: 6016 Cov.: 32 AF XY: 0.250 AC XY: 18563 AN XY: 74360

African (AFR) AF: 0.449 AC: 18609 AN: 41466

American (AMR) AF: 0.164 AC: 2507 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3470

East Asian (EAS) AF: 0.169 AC: 875 AN: 5178

South Asian (SAS) AF: 0.345 AC: 1662 AN: 4822

European-Finnish (FIN) AF: 0.159 AC: 1684 AN: 10580

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11310 AN: 67994

Other (OTH) AF: 0.229 AC: 484 AN: 2114

Alfa AF: 0.206 Hom.: 8185

Bravo AF: 0.255

Asia WGS AF: 0.279 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	5.7
DANN	Benign	0.83
PhyloP100		-2.4
Mutation Taster		=99/1	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: rs6580076; hg19: chr5-153783753; COSMIC: COSV51722267;