5-154385679-T-C

Position:

• chr5-154385679-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.939-634T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,142 control chromosomes in the GnomAD database, including 43,481 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 0.75 (43481 hom., cov: 32)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT10	NM_198321.4	c.939-634T>C		intron_variant		ENST00000297107.11	NP_938080.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT10	ENST00000297107.11	c.939-634T>C		intron_variant		1	NM_198321.4	ENSP00000297107	P1
SAP30L-AS1	ENST00000658072.1	n.202-55722A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114767 AN: 152024 Hom.: 43447 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.754

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.755 AC: 114858 AN: 152142 Hom.: 43481 Cov.: 32 AF XY: 0.751 AC XY: 55865 AN XY: 74366

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.753

Alfa AF: 0.728 Hom.: 20351

Bravo AF: 0.769

Asia WGS AF: 0.735 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.48

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: rs3734083; hg19: chr5-153765239;