rs2295926

Variant names:

• chr9-98831543-T-C
• rs2295926
• NM_024642.5:c.732-229T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-98831543-T-C
• chr9-98831543-T-G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_024642.5(GALNT12):​c.732-229T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,048 control chromosomes in the GnomAD database, including 13,119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.41 (13119 hom., cov: 32)
• Consequence: GALNT12 NM_024642.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.161
• Publications: 8 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, Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 9-98831543-T-C is Benign according to our data. Variant chr9-98831543-T-C is described in ClinVar as Benign. ClinVar VariationId is 1235687.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT12	NM_024642.5	MANE Select	c.732-229T>C		intron	N/A	NP_078918.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT12	ENST00000375011.4	TSL:1 MANE Select	c.732-229T>C		intron	N/A	ENSP00000364150.3	Q8IXK2-1
	GALNT12	ENST00000969913.1		c.732-229T>C		intron	N/A	ENSP00000639972.1
	GALNT12	ENST00000969912.1		c.732-229T>C		intron	N/A	ENSP00000639971.1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62632 AN: 151930 Hom.: 13102 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.412 AC: 62700 AN: 152048 Hom.: 13119 Cov.: 32 AF XY: 0.408 AC XY: 30304 AN XY: 74342

African (AFR) AF: 0.497 AC: 20606 AN: 41444

American (AMR) AF: 0.342 AC: 5224 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1086 AN: 5162

South Asian (SAS) AF: 0.308 AC: 1479 AN: 4808

European-Finnish (FIN) AF: 0.421 AC: 4454 AN: 10582

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27452 AN: 67980

Other (OTH) AF: 0.398 AC: 841 AN: 2112

Alfa AF: 0.394 Hom.: 22346

Bravo AF: 0.410

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.69
DANN	Benign	0.51
PhyloP100		0.16
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: rs2295926; hg19: chr9-101593825; COSMIC: COSV66662363;