5-154305684-A-G

Variant names:

• chr5-154305684-A-G
• rs6863455
• NM_198321.4:c.401+7605A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198321.4(GALNT10):​c.401+7605A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,170 control chromosomes in the GnomAD database, including 8,732 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 0.31 (8732 hom., cov: 32)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198321.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT10	NM_198321.4	MANE Select	c.401+7605A>G		intron	N/A	NP_938080.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT10	ENST00000297107.11	TSL:1 MANE Select	c.401+7605A>G		intron	N/A	ENSP00000297107.6
	GALNT10	ENST00000969502.1		c.401+7605A>G		intron	N/A	ENSP00000639561.1
	GALNT10	ENST00000917832.1		c.401+7605A>G		intron	N/A	ENSP00000587891.1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47468 AN: 152052 Hom.: 8720 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.312 AC: 47510 AN: 152170 Hom.: 8732 Cov.: 32 AF XY: 0.318 AC XY: 23620 AN XY: 74380

African (AFR) AF: 0.141 AC: 5840 AN: 41532

American (AMR) AF: 0.523 AC: 7996 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3470

East Asian (EAS) AF: 0.619 AC: 3202 AN: 5174

South Asian (SAS) AF: 0.380 AC: 1833 AN: 4828

European-Finnish (FIN) AF: 0.303 AC: 3209 AN: 10576

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23085 AN: 67990

Other (OTH) AF: 0.340 AC: 719 AN: 2112

Alfa AF: 0.349 Hom.: 1758

Bravo AF: 0.326

Asia WGS AF: 0.450 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6863455; hg19: chr5-153685244;