NM_003929.3:c.*204G>T

Variant names:

• chr1-205770138-C-A
• rs708723
• NM_003929.3:c.*204G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003929.3(RAB29):​c.*204G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000224 in 446,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000022 (0 hom.)
• Consequence: RAB29 NM_003929.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 0 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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.*204G>T		3_prime_UTR	Exon 6 of 6	NP_003920.1
	RAB29	NM_001135662.2		c.*204G>T		3_prime_UTR	Exon 6 of 6	NP_001129134.1
	RAB29	NM_001135663.2		c.*204G>T		3_prime_UTR	Exon 4 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.*204G>T		3_prime_UTR	Exon 6 of 6	ENSP00000356107.3
	RAB29	ENST00000235932.8	TSL:1	c.*204G>T		3_prime_UTR	Exon 6 of 6	ENSP00000235932.4
	RAB29	ENST00000437324.6	TSL:1	c.*204G>T		3_prime_UTR	Exon 5 of 5	ENSP00000416613.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000224 AC: 1 AN: 446484 Hom.: 0 Cov.: 3 AF XY: 0.00000423 AC XY: 1 AN XY: 236252

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 12442

American (AMR) AF: 0.00 AC: 0 AN: 19690

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13746

East Asian (EAS) AF: 0.00 AC: 0 AN: 30300

South Asian (SAS) AF: 0.0000219 AC: 1 AN: 45766

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29084

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2376

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 267400

Other (OTH) AF: 0.00 AC: 0 AN: 25680

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.35
DANN	Benign	0.76
PhyloP100		-2.3

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: rs708723; hg19: chr1-205739266;