9-98841430-C-T

Position:

• chr9-98841430-C-T

Variant summary

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

The ENST00000375011.4(GALNT12):​c.1344+1297C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,886 control chromosomes in the GnomAD database, including 12,186 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 0.40 (12186 hom., cov: 31)
• Consequence: GALNT12 ENST00000375011.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

Genes affected

GALNT12 (HGNC:19877): (polypeptide N-acetylgalactosaminyltransferase 12) This gene encodes a member of a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases, which catalyze the transfer of N-acetylgalactosamine (GalNAc) from UDP-GalNAc to a serine or threonine residue on a polypeptide acceptor in the initial step of O-linked protein glycosylation. Mutations in this gene are associated with an increased susceptibility to colorectal cancer.[provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT12	NM_024642.5	c.1344+1297C>T		intron_variant		ENST00000375011.4	NP_078918.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT12	ENST00000375011.4	c.1344+1297C>T		intron_variant		1	NM_024642.5	ENSP00000364150	P1
GALNT12	ENST00000615204.1	n.206+1297C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60080 AN: 151768 Hom.: 12194 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.396 AC: 60106 AN: 151886 Hom.: 12186 Cov.: 31 AF XY: 0.397 AC XY: 29435 AN XY: 74222

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.394

Alfa AF: 0.428 Hom.: 29128

Bravo AF: 0.393

Asia WGS AF: 0.404 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.5
DANN	Benign	0.16

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: rs10819377; hg19: chr9-101603712;