1-205775090-C-G

Variant names:

• chr1-205775090-C-G
• rs1572931
• ENST00000414729.1:c.-134G>C

Variant summary

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

The ENST00000414729.1(RAB29):​c.-134G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,068,154 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000019 (0 hom.)
• Consequence: RAB29 ENST00000414729.1 5_prime_UTR
• Scores: Splicing: ADA: 0.0003344
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• 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]

ENSG00000285521 (HGNC:):

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=-0.72).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414729.1. 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.-130-4G>C		splice_region intron	N/A	NP_003920.1
	RAB29	NM_001135663.2		c.-134G>C		5_prime_UTR	Exon 1 of 4	NP_001129135.1
	RAB29	NM_001135662.2		c.-130-4G>C		splice_region intron	N/A	NP_001129134.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB29	ENST00000414729.1	TSL:1	c.-134G>C		5_prime_UTR	Exon 1 of 5	ENSP00000402910.1
	RAB29	ENST00000367139.8	TSL:1 MANE Select	c.-130-4G>C		splice_region intron	N/A	ENSP00000356107.3
	RAB29	ENST00000235932.8	TSL:1	c.-130-4G>C		splice_region intron	N/A	ENSP00000235932.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000187 AC: 2 AN: 1068154 Hom.: 0 Cov.: 14 AF XY: 0.00 AC XY: 0 AN XY: 531618

African (AFR) AF: 0.0000842 AC: 2 AN: 23742

American (AMR) AF: 0.00 AC: 0 AN: 27506

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18686

East Asian (EAS) AF: 0.00 AC: 0 AN: 34924

South Asian (SAS) AF: 0.00 AC: 0 AN: 64416

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33826

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4762

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 813796

Other (OTH) AF: 0.00 AC: 0 AN: 46496

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.2
DANN	Benign	0.79
PhyloP100		-0.20
PromoterAI		-0.0030	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00033
SpliceAI score (max)		0.010		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: rs1572931; hg19: chr1-205744218;