rs10796

Positions:

• chr5-154418808-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198321.4(GALNT10):​c.*1836G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,180 control chromosomes in the GnomAD database, including 2,375 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 0.18 (2374 hom., cov: 31)
  • Exomes 𝑓: 0.16 (1 hom.)
• Consequence: GALNT10 NM_198321.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT10	NM_198321.4	c.*1836G>C		3_prime_UTR_variant	12/12	ENST00000297107.11	NP_938080.1
SAP30L-AS1	NR_037897.1	n.204+24554C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT10	ENST00000297107.11	c.*1836G>C		3_prime_UTR_variant	12/12	1	NM_198321.4	ENSP00000297107	P1
SAP30L-AS1	ENST00000658072.1	n.201+24554C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26974 AN: 151994 Hom.: 2370 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.197

GnomAD4 exome AF: 0.162 AC: 11 AN: 68 Hom.: 1 Cov.: 0 AF XY: 0.200 AC XY: 10 AN XY: 50

Gnomad4 FIN exome AF: 0.177

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.177 AC: 26994 AN: 152112 Hom.: 2374 Cov.: 31 AF XY: 0.179 AC XY: 13312 AN XY: 74342

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.200

Alfa AF: 0.173 Hom.: 306

Bravo AF: 0.172

Asia WGS AF: 0.253 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.70

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: rs10796; hg19: chr5-153798368; COSMIC: COSV51724096;