2-154450240-A-T

Position:

• chr2-154450240-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.1531-171A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,896 control chromosomes in the GnomAD database, including 31,595 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 0.63 (31595 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

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]

GALNT13-AS1 (HGNC:56700): (GALNT13 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT13	NM_052917.4	c.1531-171A>T		intron_variant		ENST00000392825.8
GALNT13-AS1	NR_161181.1	n.286+4298T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT13	ENST00000392825.8	c.1531-171A>T		intron_variant		2	NM_052917.4	P1
GALNT13-AS1	ENST00000434635.1	n.286+4298T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96055 AN: 151780 Hom.: 31561 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.633 AC: 96139 AN: 151896 Hom.: 31595 Cov.: 32 AF XY: 0.633 AC XY: 46949 AN XY: 74212

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.592

Alfa AF: 0.478 Hom.: 1415

Bravo AF: 0.633

Asia WGS AF: 0.712 AC: 2477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.72
DANN	Benign	0.86

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: rs707079; hg19: chr2-155306752;