rs10760260

Positions:

• chr9-122951247-T-G

Variant summary

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

The NM_012197.4(RABGAP1):​c.-49-5764T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,054 control chromosomes in the GnomAD database, including 36,721 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 0.62 (36721 hom., cov: 31)
• Consequence: RABGAP1 NM_012197.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

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]

RABGAP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RABGAP1	NM_012197.4	c.-49-5764T>G		intron_variant		ENST00000373647.9	NP_036329.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RABGAP1	ENST00000373647.9	c.-49-5764T>G		intron_variant		1	NM_012197.4	ENSP00000362751.4

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94761 AN: 151936 Hom.: 36736 Cov.: 31

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.623 AC: 94734 AN: 152054 Hom.: 36721 Cov.: 31 AF XY: 0.621 AC XY: 46151 AN XY: 74322

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.658

Alfa AF: 0.829 Hom.: 70280

Bravo AF: 0.582

Asia WGS AF: 0.511 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.72

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: rs10760260; hg19: chr9-125713526;