rs7624799

chr3-43004311-A-Gchr3-43004311-A-T

Variant summary

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

The NM_001129908.3(GASK1A):c.3+24666A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,266 control chromosomes in the GnomAD database, including 2,692 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 (2692 hom., cov: 33)
• Consequence: GASK1A NM_001129908.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GASK1A	NM_001129908.3	c.3+24666A>G		intron_variant		ENST00000430121.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GASK1A	ENST00000430121.3	c.3+24666A>G		intron_variant		5	NM_001129908.3	P1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26532 AN: 152148 Hom.: 2695 Cov.: 33

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.174 AC: 26532 AN: 152266 Hom.: 2692 Cov.: 33 AF XY: 0.174 AC XY: 12925 AN XY: 74438

Gnomad4 AFR AF: 0.0665

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.197

Alfa AF: 0.198 Hom.: 723

Bravo AF: 0.161

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.95
Dann	Benign	0.39

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: rs7624799; hg19: chr3-43045803;