rs8040116

Positions:

• chr15-49290392-C-G

Variant summary

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

The NM_002044.4(GALK2):​c.757-1935C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,196 control chromosomes in the GnomAD database, including 3,094 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 0.16 (3094 hom., cov: 33)
• Consequence: GALK2 NM_002044.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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]

GALK2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALK2	NM_002044.4	c.757-1935C>G		intron_variant		ENST00000560031.6	NP_002035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALK2	ENST00000560031.6	c.757-1935C>G		intron_variant		1	NM_002044.4	ENSP00000453129.1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24421 AN: 152078 Hom.: 3085 Cov.: 33

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0498

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0551

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.161 AC: 24452 AN: 152196 Hom.: 3094 Cov.: 33 AF XY: 0.159 AC XY: 11843 AN XY: 74416

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0498

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0551

Gnomad4 NFE AF: 0.0756

Gnomad4 OTH AF: 0.122

Alfa AF: 0.131 Hom.: 247

Bravo AF: 0.169

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.48

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: rs8040116; hg19: chr15-49582589;