rs2881373

Variant names:

• chr4-158171481-A-G
• rs2881373
• NM_001128424.2:c.-106T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 36 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128424.2. 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
	GASK1B	NM_001128424.2	MANE Select	c.-106T>C		5_prime_UTR	Exon 2 of 5	NP_001121896.1
	GASK1B	NM_001031700.3		c.-106T>C		5_prime_UTR	Exon 2 of 6	NP_001026870.2
	GASK1B	NM_016613.7		c.-106T>C		5_prime_UTR	Exon 2 of 5	NP_057697.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GASK1B	ENST00000585682.6	TSL:1 MANE Select	c.-106T>C		5_prime_UTR	Exon 2 of 5	ENSP00000465976.1
	GASK1B	ENST00000393807.9	TSL:1	c.-106T>C		5_prime_UTR	Exon 2 of 6	ENSP00000377396.4
	GASK1B	ENST00000296530.12	TSL:1	c.-106T>C		5_prime_UTR	Exon 2 of 5	ENSP00000296530.7

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

African (AFR) AF: 0.548 AC: 14357 AN: 26218

American (AMR) AF: 0.883 AC: 17642 AN: 19970

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 13534 AN: 17848

East Asian (EAS) AF: 0.959 AC: 33296 AN: 34710

South Asian (SAS) AF: 0.847 AC: 46164 AN: 54526

European-Finnish (FIN) AF: 0.840 AC: 31995 AN: 38090

Middle Eastern (MID) AF: 0.801 AC: 2650 AN: 3310

European-Non Finnish (NFE) AF: 0.850 AC: 778856 AN: 916314

Other (OTH) AF: 0.826 AC: 40433 AN: 48978

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

African (AFR) AF: 0.553 AC: 22929 AN: 41452

American (AMR) AF: 0.848 AC: 12959 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2604 AN: 3470

East Asian (EAS) AF: 0.946 AC: 4890 AN: 5170

South Asian (SAS) AF: 0.846 AC: 4079 AN: 4820

European-Finnish (FIN) AF: 0.836 AC: 8853 AN: 10594

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57824 AN: 68024

Other (OTH) AF: 0.796 AC: 1679 AN: 2110

Alfa AF: 0.807 Hom.: 71596

Bravo AF: 0.758

Asia WGS AF: 0.859 AC: 2986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.54
PhyloP100		0.63
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2881373; hg19: chr4-159092633;