rs372045538

Variant names:

• chr17-5308697-C-A
• NM_004703.6:c.38C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-5308697-C-A
• chr17-5308697-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004703.6(RABEP1):​c.38C>A​(p.Ser13Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: RABEP1 NM_004703.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.75

Genes affected

RABEP1 (HGNC:17677): (rabaptin, RAB GTPase binding effector protein 1) Enables protein domain specific binding activity and protein homodimerization activity. Involved in vesicle-mediated transport. Located in endocytic vesicle and endosome. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2526336).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RABEP1	NM_004703.6	c.38C>A	p.Ser13Tyr	missense_variant	Exon 2 of 18	ENST00000537505.6	NP_004694.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RABEP1	ENST00000537505.6	c.38C>A	p.Ser13Tyr	missense_variant	Exon 2 of 18	1	NM_004703.6	ENSP00000445408.2
RABEP1	ENST00000341923.10	c.38C>A	p.Ser13Tyr	missense_variant	Exon 2 of 17	1		ENSP00000339569.6
RABEP1	ENST00000575475.2	n.200-23252C>A		intron_variant	Intron 1 of 13	1
RABEP1	ENST00000575991.1	c.224C>A	p.Ser75Tyr	missense_variant	Exon 3 of 3	4		ENSP00000459550.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.051	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.10	T;T;.
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.42
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.82	T;D;D
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.25	T;T;T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	1.5	.;L;L
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-0.93	.;.;N
REVEL	Benign	0.069
Sift	Uncertain	0.011	.;.;D
Sift4G	Uncertain	0.0020	D;D;T
Polyphen		0.55, 0.68	.;P;P
Vest4		0.35, 0.36
MutPred		0.26		.;Gain of phosphorylation at S13 (P = 0.0524);Gain of phosphorylation at S13 (P = 0.0524);
MVP		0.24
ClinPred		0.77	D
GERP RS		5.6
Varity_R		0.28
gMVP		0.32

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-5211992;