rs11632303

Variant names:

• chr15-49238124-T-A
• rs11632303
• NM_002044.4:c.358-1097T>A

Your query was ambiguous. Multiple possible variants found:

• chr15-49238124-T-A
• chr15-49238124-T-C
• chr15-49238124-T-G

Variant summary

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

The NM_002044.4(GALK2):​c.358-1097T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,150 control chromosomes in the GnomAD database, including 2,450 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 0.17 (2450 hom., cov: 32)
• Consequence: GALK2 NM_002044.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• 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]

ENSG00000305168 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALK2	NM_002044.4	c.358-1097T>A		intron_variant	Intron 4 of 9	ENST00000560031.6	NP_002035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALK2	ENST00000560031.6	c.358-1097T>A		intron_variant	Intron 4 of 9	1	NM_002044.4	ENSP00000453129.1

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25725 AN: 152032 Hom.: 2451 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.00463

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.169 AC: 25740 AN: 152150 Hom.: 2450 Cov.: 32 AF XY: 0.170 AC XY: 12660 AN XY: 74376

African (AFR) AF: 0.102 AC: 4233 AN: 41534

American (AMR) AF: 0.165 AC: 2520 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3472

East Asian (EAS) AF: 0.00483 AC: 25 AN: 5176

South Asian (SAS) AF: 0.178 AC: 857 AN: 4818

European-Finnish (FIN) AF: 0.247 AC: 2606 AN: 10570

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14160 AN: 67976

Other (OTH) AF: 0.190 AC: 402 AN: 2114

Alfa AF: 0.104 Hom.: 178

Bravo AF: 0.159

Asia WGS AF: 0.0830 AC: 287 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.5
DANN	Benign	0.57
PhyloP100		1.5
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: rs11632303; hg19: chr15-49530321;