2-154214054-A-T

Position:

• chr2-154214054-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052917.4(GALNT13):​c.312-27976A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,116 control chromosomes in the GnomAD database, including 50,758 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 0.81 (50758 hom., cov: 31)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

Genes affected

GALNT13 (HGNC:23242): (polypeptide N-acetylgalactosaminyltransferase 13) The GALNT13 protein is a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAcT; EC 2.4.1.41) family, which initiate O-linked glycosylation of mucins (see MUC3A, MIM 158371) by the initial transfer of N-acetylgalactosamine (GalNAc) with an alpha-linkage to a serine or threonine residue.[supplied by OMIM, Apr 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT13	NM_052917.4	c.312-27976A>T		intron_variant		ENST00000392825.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT13	ENST00000392825.8	c.312-27976A>T		intron_variant		2	NM_052917.4	P1
GALNT13	ENST00000409237.5	c.312-27976A>T		intron_variant		1
GALNT13	ENST00000431076.5	c.166-21992A>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123003 AN: 151998 Hom.: 50712 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.809 AC: 123101 AN: 152116 Hom.: 50758 Cov.: 31 AF XY: 0.806 AC XY: 59938 AN XY: 74348

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.829

Alfa AF: 0.767 Hom.: 24980

Bravo AF: 0.813

Asia WGS AF: 0.875 AC: 3044 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.60

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: rs958672; hg19: chr2-155070567;