rs10987898

Positions:

• chr9-98833161-T-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• 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/exons	MANE	UniProt
GALNT12	NM_024642.5	c.917+1204T>G		intron_variant		ENST00000375011.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT12	ENST00000375011.4	c.917+1204T>G		intron_variant		1	NM_024642.5	P1
GALNT12	ENST00000610463.1	c.*348+1204T>G		intron_variant, NMD_transcript_variant		4

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

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.269

Alfa AF: 0.278 Hom.: 7747

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

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: rs10987898; hg19: chr9-101595443; COSMIC: COSV66662261; COSMIC: COSV66662261;