NM_003929.3:c.-54C>A

Variant names:

• chr1-205775010-G-T
• rs708725
• NM_003929.3:c.-54C>A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 28 publications found

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]

ENSG00000285521 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003929.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB29	NM_003929.3	MANE Select	c.-54C>A		5_prime_UTR	Exon 2 of 6	NP_003920.1
	RAB29	NM_001135662.2		c.-54C>A		5_prime_UTR	Exon 2 of 6	NP_001129134.1
	RAB29	NM_001135663.2		c.-54C>A		5_prime_UTR	Exon 1 of 4	NP_001129135.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB29	ENST00000367139.8	TSL:1 MANE Select	c.-54C>A		5_prime_UTR	Exon 2 of 6	ENSP00000356107.3
	RAB29	ENST00000235932.8	TSL:1	c.-54C>A		5_prime_UTR	Exon 2 of 6	ENSP00000235932.4
	RAB29	ENST00000414729.1	TSL:1	c.-54C>A		5_prime_UTR	Exon 1 of 5	ENSP00000402910.1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49764 AN: 151948 Hom.: 9357 Cov.: 31

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.: 37 AF XY: 0.378 AC XY: 273654 AN XY: 723072

African (AFR) AF: 0.195 AC: 6503 AN: 33404

American (AMR) AF: 0.203 AC: 9040 AN: 44628

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 10430 AN: 26048

East Asian (EAS) AF: 0.000832 AC: 33 AN: 39674

South Asian (SAS) AF: 0.160 AC: 13731 AN: 86070

European-Finnish (FIN) AF: 0.449 AC: 21515 AN: 47946

Middle Eastern (MID) AF: 0.320 AC: 1845 AN: 5758

European-Non Finnish (NFE) AF: 0.428 AC: 474781 AN: 1109442

Other (OTH) AF: 0.354 AC: 21308 AN: 60214

GnomAD4 genome AF: 0.327 AC: 49762 AN: 152066 Hom.: 9352 Cov.: 31 AF XY: 0.320 AC XY: 23802 AN XY: 74332

African (AFR) AF: 0.205 AC: 8525 AN: 41506

American (AMR) AF: 0.295 AC: 4516 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3470

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5180

South Asian (SAS) AF: 0.152 AC: 734 AN: 4820

European-Finnish (FIN) AF: 0.435 AC: 4584 AN: 10546

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28859 AN: 67930

Other (OTH) AF: 0.345 AC: 728 AN: 2108

Alfa AF: 0.310 Hom.: 2637

Bravo AF: 0.310

Asia WGS AF: 0.0760 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.3
DANN	Benign	0.67
PhyloP100		-0.22
PromoterAI		-0.052	Neutral
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: rs708725; hg19: chr1-205744138; COSMIC: COSV52521034;