rs2295926

chr9-98831543-T-Cchr9-98831543-T-G

Variant summary

Our verdict is Benign. Variant got -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

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 -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT12	NM_024642.5	c.732-229T>C		intron_variant		ENST00000375011.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT12	ENST00000375011.4	c.732-229T>C		intron_variant		1	NM_024642.5	P1
GALNT12	ENST00000610463.1	c.*163-229T>C		intron_variant, NMD_transcript_variant		4

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

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.398

Alfa AF: 0.390 Hom.: 15826

Bravo AF: 0.410

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.69
Dann	Benign	0.51

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: rs2295926; hg19: chr9-101593825; COSMIC: COSV66662363;