rs13294021

Variant names:

• chr9-125306109-G-A
• rs13294021
• NM_001282680.3:c.1116+960G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-125306109-G-A
• chr9-125306109-G-T

Variant summary

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

The NM_001282680.3(GAPVD1):​c.1116+960G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,774 control chromosomes in the GnomAD database, including 16,089 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 0.45 (16089 hom., cov: 31)
• Consequence: GAPVD1 NM_001282680.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 6 publications found

Genes affected

GAPVD1 (HGNC:23375): (GTPase activating protein and VPS9 domains 1) Enables GTPase activating protein binding activity and guanyl-nucleotide exchange factor activity. Involved in regulation of protein transport. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

GAPVD1 Gene-Disease associations (from GenCC):

• familial idiopathic steroid-resistant nephrotic syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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 (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282680.3. 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
	GAPVD1	NM_001282680.3	MANE Select	c.1116+960G>A		intron	N/A	NP_001269609.1	Q14C86-2
	GAPVD1	NM_015635.4		c.1116+960G>A		intron	N/A	NP_056450.2
	GAPVD1	NM_001282679.2		c.1116+960G>A		intron	N/A	NP_001269608.1	Q14C86-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAPVD1	ENST00000297933.11	TSL:1 MANE Select	c.1116+960G>A		intron	N/A	ENSP00000297933.6	Q14C86-2
	GAPVD1	ENST00000495955.5	TSL:1	c.1116+960G>A		intron	N/A	ENSP00000419063.1	Q14C86-1
	GAPVD1	ENST00000312123.13	TSL:1	c.1116+960G>A		intron	N/A	ENSP00000309582.9	Q14C86-4

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68839 AN: 151668 Hom.: 16082 Cov.: 31

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.454 AC: 68863 AN: 151774 Hom.: 16089 Cov.: 31 AF XY: 0.450 AC XY: 33389 AN XY: 74164

African (AFR) AF: 0.517 AC: 21375 AN: 41362

American (AMR) AF: 0.349 AC: 5315 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5164

South Asian (SAS) AF: 0.377 AC: 1812 AN: 4810

European-Finnish (FIN) AF: 0.489 AC: 5135 AN: 10506

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31230 AN: 67918

Other (OTH) AF: 0.452 AC: 950 AN: 2104

Alfa AF: 0.454 Hom.: 44059

Bravo AF: 0.443

Asia WGS AF: 0.301 AC: 1049 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	0.15
DANN	Benign	0.50
PhyloP100		-1.2
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: rs13294021; hg19: chr9-128068388;