chr9-98841430-C-T

Variant names:

• chr9-98841430-C-T
• rs10819377
• NM_024642.5:c.1344+1297C>T

Variant summary

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

The NM_024642.5(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 NM_024642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 5 publications found

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]

GALNT12 Gene-Disease associations (from GenCC):

• colorectal cancer, susceptibility to, 1

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GALNT12	NM_024642.5	c.1344+1297C>T		intron_variant	Intron 7 of 9	ENST00000375011.4	NP_078918.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT12	ENST00000375011.4	c.1344+1297C>T		intron_variant	Intron 7 of 9	1	NM_024642.5	ENSP00000364150.3
GALNT12	ENST00000615204.1	n.206+1297C>T		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.314 AC: 13008 AN: 41400

American (AMR) AF: 0.411 AC: 6280 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1244 AN: 3472

East Asian (EAS) AF: 0.375 AC: 1934 AN: 5152

South Asian (SAS) AF: 0.395 AC: 1900 AN: 4806

European-Finnish (FIN) AF: 0.435 AC: 4582 AN: 10530

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29842 AN: 67944

Other (OTH) AF: 0.394 AC: 832 AN: 2110

Alfa AF: 0.423 Hom.: 43735

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
PhyloP100		0.50
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: rs10819377; hg19: chr9-101603712;