chr9-98833161-T-G

Variant names:

• chr9-98833161-T-G
• rs10987898
• NM_024642.5:c.917+1204T>G

Variant summary

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

The NM_024642.5(GALNT12):​c.917+1204T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,928 control chromosomes in the GnomAD database, including 6,019 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 0.28 (6019 hom., cov: 31)
• Consequence: GALNT12 NM_024642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT12	NM_024642.5	c.917+1204T>G		intron_variant	Intron 4 of 9	ENST00000375011.4	NP_078918.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT12	ENST00000375011.4	c.917+1204T>G		intron_variant	Intron 4 of 9	1	NM_024642.5	ENSP00000364150.3
GALNT12	ENST00000610463.1	n.*348+1204T>G		intron_variant	Intron 3 of 3	4		ENSP00000477657.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42102 AN: 151808 Hom.: 6025 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.277 AC: 42121 AN: 151928 Hom.: 6019 Cov.: 31 AF XY: 0.282 AC XY: 20935 AN XY: 74232

African (AFR) AF: 0.243 AC: 10059 AN: 41424

American (AMR) AF: 0.322 AC: 4914 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1805 AN: 5132

South Asian (SAS) AF: 0.358 AC: 1722 AN: 4816

European-Finnish (FIN) AF: 0.303 AC: 3199 AN: 10552

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18644 AN: 67960

Other (OTH) AF: 0.269 AC: 567 AN: 2108

Alfa AF: 0.278 Hom.: 18063

Bravo AF: 0.281

Asia WGS AF: 0.369 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.67
PhyloP100		0.44
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: rs10987898; hg19: chr9-101595443; COSMIC: COSV66662261; COSMIC: COSV66662261;