rs10760152

Positions:

• chr9-121185707-A-C
• chr9-121185707-A-G
• chr9-121185707-A-T

Variant summary

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

The ENST00000373840.9(RAB14):​c.351+1246T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 151,964 control chromosomes in the GnomAD database, including 35,714 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 0.68 (35714 hom., cov: 31)
• Consequence: RAB14 ENST00000373840.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

RAB14 (HGNC:16524): (RAB14, member RAS oncogene family) RAB14 belongs to the large RAB family of low molecular mass GTPases that are involved in intracellular membrane trafficking. These proteins act as molecular switches that flip between an inactive GDP-bound state and an active GTP-bound state in which they recruit downstream effector proteins onto membranes (Junutula et al., 2004 [PubMed 15004230]).[supplied by OMIM, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB14	NM_016322.4	c.351+1246T>G		intron_variant		ENST00000373840.9	NP_057406.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB14	ENST00000373840.9	c.351+1246T>G		intron_variant		1	NM_016322.4	ENSP00000362946	P1

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103065 AN: 151846 Hom.: 35674 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.679 AC: 103159 AN: 151964 Hom.: 35714 Cov.: 31 AF XY: 0.684 AC XY: 50835 AN XY: 74302

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.920

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.702

Alfa AF: 0.682 Hom.: 9876

Bravo AF: 0.681

Asia WGS AF: 0.889 AC: 3088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.024
DANN	Benign	0.64

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: rs10760152; hg19: chr9-123947985;