1-205775090-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414729.1(RAB29):​c.-134G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,218,430 control chromosomes in the GnomAD database, including 16,463 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 0.15 (2022 hom., cov: 32)
  • Exomes 𝑓: 0.15 (14441 hom.)
• Consequence: RAB29 ENST00000414729.1 5_prime_UTR
• Scores: Splicing: ADA: 0.001650
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB29	NM_003929.3	c.-130-4G>A		splice_region_variant, intron_variant	Intron 1 of 5	ENST00000367139.8	NP_003920.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB29	ENST00000367139.8	c.-130-4G>A		splice_region_variant, intron_variant	Intron 1 of 5	1	NM_003929.3	ENSP00000356107.3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22547 AN: 152094 Hom.: 2017 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.148

GnomAD4 exome AF: 0.151 AC: 161508 AN: 1066218 Hom.: 14441 Cov.: 14 AF XY: 0.154 AC XY: 81587 AN XY: 530668

African (AFR) AF: 0.105 AC: 2482 AN: 23716

American (AMR) AF: 0.371 AC: 10176 AN: 27454

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 2385 AN: 18662

East Asian (EAS) AF: 0.342 AC: 11938 AN: 34902

South Asian (SAS) AF: 0.240 AC: 15441 AN: 64310

European-Finnish (FIN) AF: 0.112 AC: 3773 AN: 33804

Middle Eastern (MID) AF: 0.124 AC: 591 AN: 4760

European-Non Finnish (NFE) AF: 0.132 AC: 107490 AN: 812186

Other (OTH) AF: 0.156 AC: 7232 AN: 46424

GnomAD4 genome AF: 0.148 AC: 22564 AN: 152212 Hom.: 2022 Cov.: 32 AF XY: 0.150 AC XY: 11200 AN XY: 74420

African (AFR) AF: 0.105 AC: 4372 AN: 41526

American (AMR) AF: 0.267 AC: 4075 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1617 AN: 5162

South Asian (SAS) AF: 0.241 AC: 1163 AN: 4830

European-Finnish (FIN) AF: 0.105 AC: 1110 AN: 10614

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9272 AN: 68000

Other (OTH) AF: 0.147 AC: 310 AN: 2112

Alfa AF: 0.143 Hom.: 3156

Bravo AF: 0.161

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.6
DANN	Benign	0.91
PhyloP100		-0.20
PromoterAI		-0.015	Neutral
Mutation Taster		=84/16	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0017
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;