1-205769123-C-G

Variant names:

• chr1-205769123-C-G
• rs823136
• NM_003929.3:c.*1219G>C

Variant summary

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

The NM_003929.3(RAB29):​c.*1219G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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)
• Consequence: RAB29 NM_003929.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 9 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: 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=-0.81).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB29	NM_003929.3	MANE Select	c.*1219G>C		3_prime_UTR	Exon 6 of 6	NP_003920.1	O14966-1
	RAB29	NM_001135662.2		c.*1219G>C		3_prime_UTR	Exon 6 of 6	NP_001129134.1	O14966-1
	RAB29	NM_001135663.2		c.*1219G>C		3_prime_UTR	Exon 4 of 4	NP_001129135.1	O14966-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB29	ENST00000367139.8	TSL:1 MANE Select	c.*1219G>C		3_prime_UTR	Exon 6 of 6	ENSP00000356107.3	O14966-1
	RAB29	ENST00000895155.1		c.*1219G>C		3_prime_UTR	Exon 6 of 6	ENSP00000565214.1
	RAB29	ENST00000895156.1		c.*1219G>C		3_prime_UTR	Exon 6 of 6	ENSP00000565215.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.074

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: rs823136; hg19: chr1-205738251;