rs2881373

chr4-158171481-A-G

Variant summary

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

The NM_001128424.2(GASK1B):c.-106T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 1,312,100 control chromosomes in the GnomAD database, including 460,895 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 0.77 (46309 hom., cov: 32)
  • Exomes 𝑓: 0.84 (414586 hom.)
• Consequence: GASK1B NM_001128424.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625

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 Benign. Variant got -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 = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GASK1B	NM_001128424.2	c.-106T>C		5_prime_UTR_variant	2/5	ENST00000585682.6
GASK1B-AS1	NR_147407.1	n.729+1A>G		splice_donor_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GASK1B	ENST00000585682.6	c.-106T>C		5_prime_UTR_variant	2/5	1	NM_001128424.2	P1
GASK1B-AS1	ENST00000503611.5	n.729+1A>G		splice_donor_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116737 AN: 152018 Hom.: 46295 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.795

GnomAD4 exome AF: 0.844 AC: 978927 AN: 1159964 Hom.: 414586 Cov.: 15 AF XY: 0.844 AC XY: 476542 AN XY: 564326

Gnomad4 AFR exome AF: 0.548

Gnomad4 AMR exome AF: 0.883

Gnomad4 ASJ exome AF: 0.758

Gnomad4 EAS exome AF: 0.959

Gnomad4 SAS exome AF: 0.847

Gnomad4 FIN exome AF: 0.840

Gnomad4 NFE exome AF: 0.850

Gnomad4 OTH exome AF: 0.826

GnomAD4 genome AF: 0.768 AC: 116784 AN: 152136 Hom.: 46309 Cov.: 32 AF XY: 0.772 AC XY: 57386 AN XY: 74380

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.796

Alfa AF: 0.833 Hom.: 54173

Bravo AF: 0.758

Asia WGS AF: 0.859 AC: 2986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	12
Dann	Benign	0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2881373; hg19: chr4-159092633;