chr1-205769174-G-A

Variant names:

• chr1-205769174-G-A
• rs823137
• NM_003929.3:c.*1168C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 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: Benign. The variant received -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.

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.*1168C>T		3_prime_UTR	Exon 6 of 6	NP_003920.1
	RAB29	NM_001135662.2		c.*1168C>T		3_prime_UTR	Exon 6 of 6	NP_001129134.1
	RAB29	NM_001135663.2		c.*1168C>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.*1168C>T		3_prime_UTR	Exon 6 of 6	ENSP00000356107.3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.207 AC: 8575 AN: 41370

American (AMR) AF: 0.299 AC: 4492 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3468

East Asian (EAS) AF: 0.00531 AC: 27 AN: 5086

South Asian (SAS) AF: 0.161 AC: 763 AN: 4740

European-Finnish (FIN) AF: 0.442 AC: 4613 AN: 10440

Middle Eastern (MID) AF: 0.375 AC: 108 AN: 288

European-Non Finnish (NFE) AF: 0.429 AC: 28995 AN: 67646

Other (OTH) AF: 0.352 AC: 737 AN: 2094

Alfa AF: 0.389 Hom.: 9653

Bravo AF: 0.311

Asia WGS AF: 0.0760 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		-0.41
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: rs823137; hg19: chr1-205738302;