chr1-205769174-G-A

Position:

• chr1-205769174-G-A

Variant summary

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

The NM_003929.3(RAB29):​c.*1168C>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 0.331 in 151,068 control chromosomes in the GnomAD database, including 9,487 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 (9486 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: RAB29 NM_003929.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB29	NM_003929.3	c.*1168C>T		3_prime_UTR_variant	6/6	ENST00000367139.8	NP_003920.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB29	ENST00000367139.8	c.*1168C>T		3_prime_UTR_variant	6/6	1	NM_003929.3	ENSP00000356107	P1

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50012 AN: 150944 Hom.: 9492 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.00530

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.381

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.357

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 3 AN XY: 6

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.331 AC: 50007 AN: 151062 Hom.: 9486 Cov.: 32 AF XY: 0.324 AC XY: 23896 AN XY: 73742

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.00531

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.352

Alfa AF: 0.382 Hom.: 6154

Bravo AF: 0.311

Asia WGS AF: 0.0760 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.49

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: rs823137; hg19: chr1-205738302;