rs16917929

Variant names:

• chr9-98831937-A-G
• rs16917929
• NM_024642.5:c.897A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-98831937-A-G
• chr9-98831937-A-T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_024642.5(GALNT12):​c.897A>G​(p.Gln299Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00685 in 1,613,826 control chromosomes in the GnomAD database, including 673 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.037 (362 hom., cov: 32)
  • Exomes 𝑓: 0.0037 (311 hom.)
• Consequence: GALNT12 NM_024642.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:8
• Conservation: PhyloP100: -0.562
• Publications: 2 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 -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 9-98831937-A-G is Benign according to our data. Variant chr9-98831937-A-G is described in ClinVar as Benign. ClinVar VariationId is 416216.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.562 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024642.5. 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
	GALNT12	NM_024642.5	MANE Select	c.897A>G	p.Gln299Gln	synonymous	Exon 4 of 10	NP_078918.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT12	ENST00000375011.4	TSL:1 MANE Select	c.897A>G	p.Gln299Gln	synonymous	Exon 4 of 10	ENSP00000364150.3
	GALNT12	ENST00000610463.1	TSL:4	n.*328A>G		non_coding_transcript_exon	Exon 3 of 4	ENSP00000477657.1
	GALNT12	ENST00000610463.1	TSL:4	n.*328A>G		3_prime_UTR	Exon 3 of 4	ENSP00000477657.1

Frequencies

GnomAD3 genomes AF: 0.0368 AC: 5598 AN: 151970 Hom.: 360 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0105

Gnomad ASJ AF: 0.00404

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000221

Gnomad OTH AF: 0.0311

GnomAD2 exomes AF: 0.00959 AC: 2409 AN: 251078 AF XY: 0.00686

Gnomad AFR exome AF: 0.131

Gnomad AMR exome AF: 0.00547

Gnomad ASJ exome AF: 0.00357

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000194

Gnomad OTH exome AF: 0.00490

GnomAD4 exome AF: 0.00373 AC: 5450 AN: 1461738 Hom.: 311 Cov.: 32 AF XY: 0.00314 AC XY: 2285 AN XY: 727164

African (AFR) AF: 0.133 AC: 4456 AN: 33468

American (AMR) AF: 0.00631 AC: 282 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.00344 AC: 90 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.000302 AC: 26 AN: 86220

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53416

Middle Eastern (MID) AF: 0.00243 AC: 14 AN: 5768

European-Non Finnish (NFE) AF: 0.0000701 AC: 78 AN: 1111934

Other (OTH) AF: 0.00835 AC: 504 AN: 60388

GnomAD4 genome AF: 0.0369 AC: 5608 AN: 152088 Hom.: 362 Cov.: 32 AF XY: 0.0359 AC XY: 2671 AN XY: 74348

African (AFR) AF: 0.129 AC: 5347 AN: 41452

American (AMR) AF: 0.0105 AC: 161 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00404 AC: 14 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5150

South Asian (SAS) AF: 0.000830 AC: 4 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10596

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000221 AC: 15 AN: 68006

Other (OTH) AF: 0.0308 AC: 65 AN: 2112

Alfa AF: 0.0114 Hom.: 206

Bravo AF: 0.0413

Asia WGS AF: 0.0120 AC: 44 AN: 3478

EpiCase AF: 0.000218

EpiControl AF: 0.000356

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	3	not provided (3)
-	-	2	not specified (2)
-	-	1	Colorectal cancer, susceptibility to, 1 (1)
-	-	1	GALNT12-related disorder (1)
-	-	1	Hereditary cancer-predisposing syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.47
DANN	Benign	0.33
PhyloP100		-0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
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: rs16917929; hg19: chr9-101594219;