9-122947044-A-G

Position:

• chr9-122947044-A-G

Variant summary

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

The NM_012197.4(RABGAP1):​c.-50+5951A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,946 control chromosomes in the GnomAD database, including 13,436 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 0.38 (13436 hom., cov: 31)
• Consequence: RABGAP1 NM_012197.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466

Genes affected

RABGAP1 (HGNC:17155): (RAB GTPase activating protein 1) Enables GTPase activator activity and small GTPase binding activity. Involved in regulation of GTPase activity. Located in cytosol. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RABGAP1	NM_012197.4	c.-50+5951A>G		intron_variant		ENST00000373647.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RABGAP1	ENST00000373647.9	c.-50+5951A>G		intron_variant		1	NM_012197.4	P1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57622 AN: 151828 Hom.: 13441 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.379 AC: 57611 AN: 151946 Hom.: 13436 Cov.: 31 AF XY: 0.382 AC XY: 28375 AN XY: 74260

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.390

Alfa AF: 0.477 Hom.: 25386

Bravo AF: 0.352

Asia WGS AF: 0.401 AC: 1396 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.55

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: rs10818768; hg19: chr9-125709323;