chr5-154419605-T-C

Position:

• chr5-154419605-T-C

Variant summary

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

The NM_198321.4(GALNT10):​c.*2633T>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 0.28 in 152,102 control chromosomes in the GnomAD database, including 6,164 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 0.28 (6160 hom., cov: 32)
  • Exomes 𝑓: 0.41 (4 hom.)
• Consequence: GALNT10 NM_198321.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT10	NM_198321.4	c.*2633T>C		3_prime_UTR_variant	12/12	ENST00000297107.11	NP_938080.1
SAP30L-AS1	NR_037897.1	n.204+23757A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT10	ENST00000297107.11	c.*2633T>C		3_prime_UTR_variant	12/12	1	NM_198321.4	ENSP00000297107.6

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42477 AN: 151950 Hom.: 6152 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.412 AC: 14 AN: 34 Hom.: 4 Cov.: 0 AF XY: 0.500 AC XY: 11 AN XY: 22

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.433

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.280 AC: 42513 AN: 152068 Hom.: 6160 Cov.: 32 AF XY: 0.282 AC XY: 20986 AN XY: 74340

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.303

Alfa AF: 0.278 Hom.: 5727

Bravo AF: 0.270

Asia WGS AF: 0.382 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.28
DANN	Benign	0.56

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: rs2277937; hg19: chr5-153799165; COSMIC: COSV51724106; COSMIC: COSV51724106;