3-43029355-C-T

Variant names:

• chr3-43029355-C-T
• rs704903
• NM_001129908.3:c.4-2912C>T

Variant summary

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

The NM_001129908.3(GASK1A):​c.4-2912C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 151,964 control chromosomes in the GnomAD database, including 49,262 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 0.80 (49262 hom., cov: 29)
• Consequence: GASK1A NM_001129908.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.973
• Publications: 2 publications found

Genes affected

GASK1A (HGNC:24485): (golgi associated kinase 1A) Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000273291 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GASK1A	NM_001129908.3	c.4-2912C>T		intron_variant	Intron 1 of 4	ENST00000430121.3	NP_001123380.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GASK1A	ENST00000430121.3	c.4-2912C>T		intron_variant	Intron 1 of 4	5	NM_001129908.3	ENSP00000407301.2
ENSG00000273291	ENST00000446977.2	c.278-2912C>T		intron_variant	Intron 4 of 4	4		ENSP00000477043.1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122079 AN: 151844 Hom.: 49217 Cov.: 29

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.804 AC: 122188 AN: 151964 Hom.: 49262 Cov.: 29 AF XY: 0.805 AC XY: 59759 AN XY: 74246

African (AFR) AF: 0.860 AC: 35644 AN: 41442

American (AMR) AF: 0.834 AC: 12755 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2637 AN: 3470

East Asian (EAS) AF: 0.736 AC: 3787 AN: 5148

South Asian (SAS) AF: 0.801 AC: 3841 AN: 4798

European-Finnish (FIN) AF: 0.792 AC: 8365 AN: 10564

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52541 AN: 67936

Other (OTH) AF: 0.792 AC: 1676 AN: 2116

Alfa AF: 0.788 Hom.: 129319

Bravo AF: 0.811

Asia WGS AF: 0.762 AC: 2650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.37
PhyloP100		-0.97
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: rs704903; hg19: chr3-43070847;