rs16962243

chr15-49270535-C-T

Variant summary

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

The NM_002044.4(GALK2):c.505-11452C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,194 control chromosomes in the GnomAD database, including 3,424 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 0.18 (3424 hom., cov: 33)
• Consequence: GALK2 NM_002044.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

Genes affected

GALK2 (HGNC:4119): (galactokinase 2) This gene encodes a highly efficient N-acetylgalactosamine (GalNAc) kinase, which has galactokinase activity when galactose is present at high concentrations. The encoded protein is a member of the GHMP kinase family. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALK2	NM_002044.4	c.505-11452C>T		intron_variant		ENST00000560031.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALK2	ENST00000560031.6	c.505-11452C>T		intron_variant		1	NM_002044.4	P1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28095 AN: 152076 Hom.: 3422 Cov.: 33

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.185 AC: 28102 AN: 152194 Hom.: 3424 Cov.: 33 AF XY: 0.189 AC XY: 14050 AN XY: 74388

Gnomad4 AFR AF: 0.0456

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.214

Alfa AF: 0.214 Hom.: 7287

Bravo AF: 0.186

Asia WGS AF: 0.272 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.0
Dann	Benign	0.69

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: rs16962243; hg19: chr15-49562732;