rs1060504772

Variant names:

• chr9-98807842-C-G
• rs1060504772
• NM_024642.5:c.144C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-98807842-C-G
• chr9-98807842-C-T
• chr9-98807842-C-A

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_024642.5(GALNT12):​c.144C>G​(p.Ala48Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000733 in 1,009,410 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A48A) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.00012 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000065 (0 hom.)
• Consequence: GALNT12 NM_024642.5 synonymous
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -3.11
• Publications: 0 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 -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant 9-98807842-C-G is Benign according to our data. Variant chr9-98807842-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 416215.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-3.11 with no splicing effect.
• BS2: High AC in GnomAd4 at 18 AD gene.

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.144C>G	p.Ala48Ala	synonymous	Exon 1 of 10	NP_078918.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT12	ENST00000375011.4	TSL:1 MANE Select	c.144C>G	p.Ala48Ala	synonymous	Exon 1 of 10	ENSP00000364150.3	Q8IXK2-1
	GALNT12	ENST00000969913.1		c.144C>G	p.Ala48Ala	synonymous	Exon 1 of 11	ENSP00000639972.1
	GALNT12	ENST00000969912.1		c.144C>G	p.Ala48Ala	synonymous	Exon 1 of 11	ENSP00000639971.1

Frequencies

GnomAD3 genomes AF: 0.000123 AC: 18 AN: 146558 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000490

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000678

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000759

Gnomad OTH AF: 0.000496

GnomAD4 exome AF: 0.0000649 AC: 56 AN: 862852 Hom.: 0 Cov.: 30 AF XY: 0.0000672 AC XY: 27 AN XY: 401546

African (AFR) AF: 0.00 AC: 0 AN: 16332

American (AMR) AF: 0.000986 AC: 2 AN: 2028

Ashkenazi Jewish (ASJ) AF: 0.000511 AC: 3 AN: 5874

East Asian (EAS) AF: 0.00 AC: 0 AN: 4964

South Asian (SAS) AF: 0.00 AC: 0 AN: 17546

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3404

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1738

European-Non Finnish (NFE) AF: 0.0000627 AC: 49 AN: 781960

Other (OTH) AF: 0.0000690 AC: 2 AN: 29006

GnomAD4 genome AF: 0.000123 AC: 18 AN: 146558 Hom.: 0 Cov.: 32 AF XY: 0.000182 AC XY: 13 AN XY: 71280

African (AFR) AF: 0.0000490 AC: 2 AN: 40810

American (AMR) AF: 0.000678 AC: 10 AN: 14752

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3386

East Asian (EAS) AF: 0.00 AC: 0 AN: 5066

South Asian (SAS) AF: 0.00 AC: 0 AN: 4802

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8600

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 310

European-Non Finnish (NFE) AF: 0.0000759 AC: 5 AN: 65904

Other (OTH) AF: 0.000496 AC: 1 AN: 2018

Alfa AF: 0.000142 Hom.: 0

Bravo AF: 0.000325

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	GALNT12-related disorder (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.7
DANN	Benign	0.37
PhyloP100		-3.1
PromoterAI		-0.0090	Neutral

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: rs1060504772; hg19: chr9-101570124;