rs16962243

Variant names:

• chr15-49270535-C-T
• rs16962243
• NM_002044.4:c.505-11452C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

ENSG00000305168 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GALK2	NM_002044.4	c.505-11452C>T		intron_variant	Intron 5 of 9	ENST00000560031.6	NP_002035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALK2	ENST00000560031.6	c.505-11452C>T		intron_variant	Intron 5 of 9	1	NM_002044.4	ENSP00000453129.1

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

African (AFR) AF: 0.0456 AC: 1893 AN: 41556

American (AMR) AF: 0.309 AC: 4716 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1761 AN: 5164

South Asian (SAS) AF: 0.244 AC: 1178 AN: 4826

European-Finnish (FIN) AF: 0.226 AC: 2387 AN: 10572

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14852 AN: 68004

Other (OTH) AF: 0.214 AC: 452 AN: 2110

Alfa AF: 0.208 Hom.: 11672

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
PhyloP100		0.054
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16962243; hg19: chr15-49562732;