rs823136

Positions:

• chr1-205769123-C-A
• chr1-205769123-C-G
• chr1-205769123-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.*1219G>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 0.876 in 152,186 control chromosomes in the GnomAD database, including 59,558 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 0.88 (59553 hom., cov: 32)
  • Exomes 𝑓: 1.0 (5 hom.)
• Consequence: RAB29 NM_003929.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB29	NM_003929.3	c.*1219G>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.*1219G>T		3_prime_UTR_variant	6/6	1	NM_003929.3	ENSP00000356107.3

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133269 AN: 152058 Hom.: 59527 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.885

GnomAD4 exome AF: 1.00 AC: 10 AN: 10 Hom.: 5 Cov.: 0 AF XY: 1.00 AC XY: 8 AN XY: 8

Gnomad4 AFR exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.876 AC: 133353 AN: 152176 Hom.: 59553 Cov.: 32 AF XY: 0.876 AC XY: 65180 AN XY: 74424

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.893

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.886

Alfa AF: 0.948 Hom.: 117315

Bravo AF: 0.860

Asia WGS AF: 0.865 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.81

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: rs823136; hg19: chr1-205738251;