rs1864299

Variant names:

• chr15-49315655-T-C
• rs1864299
• NM_002044.4:c.968-3949T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560031.6(GALK2):​c.968-3949T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,000 control chromosomes in the GnomAD database, including 13,079 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 0.41 (13079 hom., cov: 32)
• Consequence: GALK2 ENST00000560031.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560031.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALK2	NM_002044.4	MANE Select	c.968-3949T>C		intron	N/A	NP_002035.1
	GALK2	NM_001001556.3		c.935-3949T>C		intron	N/A	NP_001001556.1
	GALK2	NM_001289030.2		c.896-3949T>C		intron	N/A	NP_001275959.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALK2	ENST00000560031.6	TSL:1 MANE Select	c.968-3949T>C		intron	N/A	ENSP00000453129.1
	GALK2	ENST00000327171.7	TSL:1	c.935-3949T>C		intron	N/A	ENSP00000316632.3
	GALK2	ENST00000396509.6	TSL:2	c.896-3949T>C		intron	N/A	ENSP00000379766.2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62668 AN: 151882 Hom.: 13073 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.412 AC: 62690 AN: 152000 Hom.: 13079 Cov.: 32 AF XY: 0.410 AC XY: 30488 AN XY: 74300

African (AFR) AF: 0.430 AC: 17845 AN: 41486

American (AMR) AF: 0.341 AC: 5213 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1610 AN: 3466

East Asian (EAS) AF: 0.357 AC: 1838 AN: 5150

South Asian (SAS) AF: 0.398 AC: 1915 AN: 4810

European-Finnish (FIN) AF: 0.393 AC: 4153 AN: 10570

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28784 AN: 67932

Other (OTH) AF: 0.371 AC: 782 AN: 2106

Alfa AF: 0.427 Hom.: 2356

Bravo AF: 0.407

Asia WGS AF: 0.392 AC: 1364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	10
DANN	Benign	0.84
PhyloP100		0.46
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: rs1864299; hg19: chr15-49607852;