rs10760152

Variant names:

• chr9-121185707-A-C
• rs10760152
• NM_016322.4:c.351+1246T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_016322.4(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 NM_016322.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 5 publications found

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]

RAB14 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: AD Classification: MODERATE Submitted by: G2P

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016322.4. 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
	RAB14	NM_016322.4	MANE Select	c.351+1246T>G		intron	N/A	NP_057406.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB14	ENST00000373840.9	TSL:1 MANE Select	c.351+1246T>G		intron	N/A	ENSP00000362946.4	P61106
	RAB14	ENST00000703999.1		c.351+1246T>G		intron	N/A	ENSP00000515613.1	P61106
	RAB14	ENST00000704000.1		c.351+1246T>G		intron	N/A	ENSP00000515614.1	P61106

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

African (AFR) AF: 0.567 AC: 23473 AN: 41410

American (AMR) AF: 0.765 AC: 11680 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2447 AN: 3466

East Asian (EAS) AF: 0.956 AC: 4948 AN: 5176

South Asian (SAS) AF: 0.920 AC: 4434 AN: 4822

European-Finnish (FIN) AF: 0.657 AC: 6941 AN: 10572

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46868 AN: 67942

Other (OTH) AF: 0.702 AC: 1479 AN: 2108

Alfa AF: 0.684 Hom.: 12648

Bravo AF: 0.681

Asia WGS AF: 0.889 AC: 3088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.024
DANN	Benign	0.64
PhyloP100		-2.0
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: rs10760152; hg19: chr9-123947985;