Genetic Variant RAB29:c.-54C>A (chr1-205775010-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003929.3(RAB29):c.-54C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 1,605,250 control chromosomes in the GnomAD database, including 125,338 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 0.33 ( 9352 hom., cov: 31)

Exomes 𝑓: 0.38 ( 115986 hom. )

Consequence

RAB29
NM_003929.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.220

Variant links:

Genes affected

RAB29 (HGNC:9789): (RAB29, member RAS oncogene family) Enables several functions, including dynein complex binding activity; guanyl ribonucleotide binding activity; and kinesin binding activity. Involved in several processes, including positive regulation of T cell receptor signaling pathway; positive regulation of receptor recycling; and toxin transport. Located in several cellular components, including Golgi apparatus; endosome; and vacuole. [provided by Alliance of Genome Resources, Apr 2022]

RAB29 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB29	NM_003929.3 link	c.-54C>A		5_prime_UTR_variant	Exon 2 of 6	ENST00000367139.8	NP_003920.1	O14966-1Q6FGU7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB29	ENST00000367139.8 link	c.-54C>A		5_prime_UTR_variant	Exon 2 of 6	1	NM_003929.3	ENSP00000356107.3		O14966-1

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49764

AN:

151948

Hom.:

9357

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.296

Gnomad ASJ

AF:

0.397

Gnomad EAS

AF:

0.00327

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.425

Gnomad OTH

AF:

0.349

GnomAD4 exome

AF:

0.385

AC:

559186

AN:

1453184

Hom.:

115986

Cov.:

AF XY:

0.378

AC XY:

273654

AN XY:

723072

show subpopulations

Gnomad4 AFR exome

AF:

0.195

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.400

Gnomad4 EAS exome

AF:

0.000832

Gnomad4 SAS exome

AF:

0.160

Gnomad4 FIN exome

AF:

0.449

Gnomad4 NFE exome

AF:

0.428

Gnomad4 OTH exome

AF:

0.354

GnomAD4 genome

AF:

0.327

AC:

49762

AN:

152066

Hom.:

9352

Cov.:

AF XY:

0.320

AC XY:

23802

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.295

Gnomad4 ASJ

AF:

0.397

Gnomad4 EAS

AF:

0.00328

Gnomad4 SAS

AF:

0.152

Gnomad4 FIN

AF:

0.435

Gnomad4 NFE

AF:

0.425

Gnomad4 OTH

AF:

0.345

Alfa

AF:

0.279

Hom.:

1036

Bravo

AF:

0.310

Asia WGS

AF:

0.0760

AC:

266

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.3

DANN

Benign

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over