rs1026467510

Variant names:

• chr4-158170991-G-A
• rs1026467510
• NM_001128424.2:c.385C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-158170991-G-A
• chr4-158170991-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001128424.2(GASK1B):​c.385C>T​(p.Arg129Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: GASK1B NM_001128424.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.39

Genes affected

GASK1B (HGNC:25312): (golgi associated kinase 1B) Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

GASK1B-AS1 (HGNC:53132): (GASK1B antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.25587225).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GASK1B	NM_001128424.2	c.385C>T	p.Arg129Cys	missense_variant	Exon 2 of 5	ENST00000585682.6	NP_001121896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GASK1B	ENST00000585682.6	c.385C>T	p.Arg129Cys	missense_variant	Exon 2 of 5	1	NM_001128424.2	ENSP00000465976.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.072	T
BayesDel_noAF	Benign	-0.34
CADD	Uncertain	25
DANN	Pathogenic	1.0
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.56
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Uncertain	0.95	.;D;D;D
M_CAP	Benign	0.021	T
MetaRNN	Benign	0.26	T;T;T;T
MetaSVM	Benign	-0.97	T
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	-2.0	.;N;N;.
REVEL	Benign	0.078
Sift	Uncertain	0.0070	.;D;D;.
Sift4G	Uncertain	0.015	D;D;D;D
Vest4		0.43
MutPred		0.24		Gain of methylation at K128 (P = 0.0528);Gain of methylation at K128 (P = 0.0528);Gain of methylation at K128 (P = 0.0528);Gain of methylation at K128 (P = 0.0528);
MVP		0.48
MPC		0.65
ClinPred		0.94	D
GERP RS		5.0
gMVP		0.34

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: rs1026467510; hg19: chr4-159092143;