rs3822711

Positions:

• chr5-154417735-C-T

Variant summary

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

The NM_198321.4(GALNT10):​c.*763C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,370 control chromosomes in the GnomAD database, including 739 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 0.081 (739 hom., cov: 32)
  • Exomes 𝑓: 0.11 (0 hom.)
• Consequence: GALNT10 NM_198321.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT10	NM_198321.4	c.*763C>T		3_prime_UTR_variant	12/12	ENST00000297107.11
SAP30L-AS1	NR_037897.1	n.205-24721G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT10	ENST00000297107.11	c.*763C>T		3_prime_UTR_variant	12/12	1	NM_198321.4	P1
SAP30L-AS1	ENST00000658072.1	n.201+25627G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12315 AN: 152148 Hom.: 739 Cov.: 32

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.0407

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0852

GnomAD4 exome AF: 0.106 AC: 11 AN: 104 Hom.: 0 Cov.: 0 AF XY: 0.128 AC XY: 10 AN XY: 78

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0930

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.0809 AC: 12317 AN: 152266 Hom.: 739 Cov.: 32 AF XY: 0.0822 AC XY: 6122 AN XY: 74450

Gnomad4 AFR AF: 0.0193

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0969 Hom.: 755

Bravo AF: 0.0749

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.4
DANN	Benign	0.79

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: rs3822711; hg19: chr5-153797295;