1-230254256-A-G

Position:

• chr1-230254256-A-G

Variant summary

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

The NM_004481.5(GALNT2):​c.1010-962A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,146 control chromosomes in the GnomAD database, including 47,464 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 0.79 (47464 hom., cov: 32)
• Consequence: GALNT2 NM_004481.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

Genes affected

GALNT2 (HGNC:4124): (polypeptide N-acetylgalactosaminyltransferase 2) This gene encodes a member of the glycosyltransferase 2 protein family. Members of this family initiate mucin-type O-glycoslation of peptides in the Golgi apparatus. The encoded protein may be involved in O-linked glycosylation of the immunoglobulin A1 hinge region. This gene may influence triglyceride levels, and may be involved Type 2 diabetes, as well as several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT2	NM_004481.5	c.1010-962A>G		intron_variant		ENST00000366672.5	NP_004472.1
GALNT2	NM_001291866.2	c.896-962A>G		intron_variant			NP_001278795.1
GALNT2	XM_017000964.3	c.917-962A>G		intron_variant			XP_016856453.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT2	ENST00000366672.5	c.1010-962A>G		intron_variant		1	NM_004481.5	ENSP00000355632	P1

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119414 AN: 152028 Hom.: 47407 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.786 AC: 119530 AN: 152146 Hom.: 47464 Cov.: 32 AF XY: 0.787 AC XY: 58501 AN XY: 74370

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.779

Alfa AF: 0.730 Hom.: 46685

Bravo AF: 0.801

Asia WGS AF: 0.864 AC: 3004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.33

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: rs901675; hg19: chr1-230390002;