rs708723

chr1-205770138-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003929.3(RAB29):c.*204G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 597,904 control chromosomes in the GnomAD database, including 83,283 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 0.46 (17717 hom., cov: 33)
  • Exomes 𝑓: 0.54 (65566 hom.)
• Consequence: RAB29 NM_003929.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB29	NM_003929.3	c.*204G>A		3_prime_UTR_variant	6/6	ENST00000367139.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB29	ENST00000367139.8	c.*204G>A		3_prime_UTR_variant	6/6	1	NM_003929.3	P1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70047 AN: 151990 Hom.: 17714 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.537 AC: 239578 AN: 445794 Hom.: 65566 Cov.: 3 AF XY: 0.538 AC XY: 126832 AN XY: 235878

Gnomad4 AFR exome AF: 0.245

Gnomad4 AMR exome AF: 0.395

Gnomad4 ASJ exome AF: 0.590

Gnomad4 EAS exome AF: 0.528

Gnomad4 SAS exome AF: 0.519

Gnomad4 FIN exome AF: 0.584

Gnomad4 NFE exome AF: 0.559

Gnomad4 OTH exome AF: 0.521

GnomAD4 genome AF: 0.461 AC: 70059 AN: 152110 Hom.: 17717 Cov.: 33 AF XY: 0.463 AC XY: 34399 AN XY: 74376

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.490

Alfa AF: 0.540 Hom.: 28507

Bravo AF: 0.436

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.52
Dann	Benign	0.77

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

Other links and lift over

dbSNP: rs708723; hg19: chr1-205739266;