1-205770138-C-T

Variant names:

• chr1-205770138-C-T
• rs708723
• NM_003929.3:c.*204G>A

Variant summary

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

The NM_003929.3(RAB29):​c.*204G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 597,904 control chromosomes in the GnomAD database, including 83,283 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 0.46 (17717 hom., cov: 33)
  • Exomes 𝑓: 0.54 (65566 hom.)
• Consequence: RAB29 NM_003929.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 62 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB29	NM_003929.3	c.*204G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000367139.8	NP_003920.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB29	ENST00000367139.8	c.*204G>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_003929.3	ENSP00000356107.3

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70047 AN: 151990 Hom.: 17714 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.537 AC: 239578 AN: 445794 Hom.: 65566 Cov.: 3 AF XY: 0.538 AC XY: 126832 AN XY: 235878

African (AFR) AF: 0.245 AC: 3041 AN: 12424

American (AMR) AF: 0.395 AC: 7759 AN: 19666

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 8099 AN: 13722

East Asian (EAS) AF: 0.528 AC: 15960 AN: 30246

South Asian (SAS) AF: 0.519 AC: 23730 AN: 45738

European-Finnish (FIN) AF: 0.584 AC: 16948 AN: 29032

Middle Eastern (MID) AF: 0.622 AC: 1474 AN: 2370

European-Non Finnish (NFE) AF: 0.559 AC: 149200 AN: 266956

Other (OTH) AF: 0.521 AC: 13367 AN: 25640

GnomAD4 genome AF: 0.461 AC: 70059 AN: 152110 Hom.: 17717 Cov.: 33 AF XY: 0.463 AC XY: 34399 AN XY: 74376

African (AFR) AF: 0.247 AC: 10253 AN: 41506

American (AMR) AF: 0.441 AC: 6741 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3472

East Asian (EAS) AF: 0.542 AC: 2797 AN: 5162

South Asian (SAS) AF: 0.527 AC: 2543 AN: 4824

European-Finnish (FIN) AF: 0.591 AC: 6248 AN: 10568

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37745 AN: 67986

Other (OTH) AF: 0.490 AC: 1035 AN: 2112

Alfa AF: 0.518 Hom.: 44988

Bravo AF: 0.436

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.52
DANN	Benign	0.77
PhyloP100		-2.3
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: rs708723; hg19: chr1-205739266;