rs7624799

Variant names:

• chr3-43004311-A-G
• rs7624799
• NM_001129908.3:c.3+24666A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-43004311-A-G
• chr3-43004311-A-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.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
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001129908.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GASK1A	NM_001129908.3	MANE Select	c.3+24666A>G		intron	N/A	NP_001123380.2	Q9UFP1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GASK1A	ENST00000430121.3	TSL:5 MANE Select	c.3+24666A>G		intron	N/A	ENSP00000407301.2	Q9UFP1
	ENSG00000273291	ENST00000446977.2	TSL:4	c.278-27956A>G		intron	N/A	ENSP00000477043.1	V9GYS6
	GASK1A	ENST00000434206.1	TSL:1	n.52+24947A>G		intron	N/A

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

African (AFR) AF: 0.0665 AC: 2763 AN: 41578

American (AMR) AF: 0.147 AC: 2248 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5180

South Asian (SAS) AF: 0.189 AC: 913 AN: 4824

European-Finnish (FIN) AF: 0.234 AC: 2478 AN: 10604

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15603 AN: 67992

Other (OTH) AF: 0.197 AC: 416 AN: 2108

Alfa AF: 0.199 Hom.: 1287

Bravo AF: 0.161

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.39
PhyloP100		-0.95
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: rs7624799; hg19: chr3-43045803;