rs1572931

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-205775090-C-A
• chr1-205775090-C-G
• chr1-205775090-C-T

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.-130-4G>T variant causes a splice region, intron 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. 2/2 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RAB29 NM_003929.3 splice_region, intron
• Scores: Splicing: ADA: 0.001398
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 22 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=-0.67).

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.-130-4G>T		splice_region intron	N/A	NP_003920.1	O14966-1
	RAB29	NM_001135663.2		c.-134G>T		5_prime_UTR	Exon 1 of 4	NP_001129135.1	O14966-2
	RAB29	NM_001135662.2		c.-130-4G>T		splice_region intron	N/A	NP_001129134.1	O14966-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB29	ENST00000414729.1	TSL:1	c.-134G>T		5_prime_UTR	Exon 1 of 5	ENSP00000402910.1	O14966-1
	RAB29	ENST00000367139.8	TSL:1 MANE Select	c.-130-4G>T		splice_region intron	N/A	ENSP00000356107.3	O14966-1
	RAB29	ENST00000235932.8	TSL:1	c.-130-4G>T		splice_region intron	N/A	ENSP00000235932.4	O14966-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1068152 Hom.: 0 Cov.: 14 AF XY: 0.00 AC XY: 0 AN XY: 531618

African (AFR) AF: 0.00 AC: 0 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: 813794

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	-0.67
CADD	Benign	9.7
DANN	Benign	0.87
PhyloP100		-0.20
PromoterAI		-0.035	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0014
SpliceAI score (max)		0.050		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;