rs10912765

chr1-174322812-C-G

Variant summary

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

The NM_001366446.1(RABGAP1L):c.1465+17685C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,902 control chromosomes in the GnomAD database, including 6,573 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 0.28 (6573 hom., cov: 32)
• Consequence: RABGAP1L NM_001366446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

RABGAP1L (HGNC:24663): (RAB GTPase activating protein 1 like) Enables GTPase activator activity and small GTPase binding activity. Acts upstream of or within regulation of protein localization. Located in Golgi apparatus; early endosome; and nucleus. [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 (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RABGAP1L	NM_001366446.1	c.1465+17685C>G		intron_variant		ENST00000681986.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RABGAP1L	ENST00000681986.1	c.1465+17685C>G		intron_variant			NM_001366446.1	P2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42681 AN: 151784 Hom.: 6556 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.281 AC: 42747 AN: 151902 Hom.: 6573 Cov.: 32 AF XY: 0.282 AC XY: 20897 AN XY: 74222

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.0684

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.275

Alfa AF: 0.257 Hom.: 775

Bravo AF: 0.288

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.92
Dann	Benign	0.70

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: rs10912765; hg19: chr1-174291950;