rs6580076

Positions:

• chr5-154404193-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_198321.4(GALNT10):​c.1146C>T​(p.Ala382=) 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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GALNT10	NM_198321.4	c.1146C>T	p.Ala382=	synonymous_variant	8/12	ENST00000297107.11
SAP30L-AS1	NR_037897.1	n.205-11179G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT10	ENST00000297107.11	c.1146C>T	p.Ala382=	synonymous_variant	8/12	1	NM_198321.4	P1
SAP30L-AS1	ENST00000658072.1	n.201+39169G>A		intron_variant, non_coding_transcript_variant

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

GnomAD3 exomes AF: 0.205 AC: 48889 AN: 238802 Hom.: 6050 AF XY: 0.210 AC XY: 26971 AN XY: 128730

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 SAS exome AF: 0.349

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

Gnomad4 AFR exome AF: 0.449

Gnomad4 AMR exome AF: 0.135

Gnomad4 ASJ exome AF: 0.187

Gnomad4 EAS exome AF: 0.166

Gnomad4 SAS exome AF: 0.340

Gnomad4 FIN exome AF: 0.149

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.203

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

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.229

Alfa AF: 0.191 Hom.: 5372

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

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

Other links and lift over

dbSNP: rs6580076; hg19: chr5-153783753; COSMIC: COSV51722267;