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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002044.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALK2	NM_002044.4	MANE Select	c.505-11452C>T		intron	N/A	NP_002035.1	Q01415-1
	GALK2	NM_001001556.3		c.472-11452C>T		intron	N/A	NP_001001556.1	Q01415-2
	GALK2	NM_001289030.2		c.433-11452C>T		intron	N/A	NP_001275959.1	B7ZAX5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALK2	ENST00000560031.6	TSL:1 MANE Select	c.505-11452C>T		intron	N/A	ENSP00000453129.1	Q01415-1
	GALK2	ENST00000327171.7	TSL:1	c.472-11452C>T		intron	N/A	ENSP00000316632.3	Q01415-2
	GALK2	ENST00000968619.1		c.505-11437C>T		intron	N/A	ENSP00000638678.1

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 v4.9

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;