rs823136

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-205769123-C-A
• chr1-205769123-C-G
• chr1-205769123-C-T

Variant summary

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

The NM_003929.3(RAB29):​c.*1219G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,186 control chromosomes in the GnomAD database, including 59,558 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 0.88 (59553 hom., cov: 32)
  • Exomes 𝑓: 1.0 (5 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

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>T		3_prime_UTR	Exon 6 of 6	NP_003920.1	O14966-1
	RAB29	NM_001135662.2		c.*1219G>T		3_prime_UTR	Exon 6 of 6	NP_001129134.1	O14966-1
	RAB29	NM_001135663.2		c.*1219G>T		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>T		3_prime_UTR	Exon 6 of 6	ENSP00000356107.3	O14966-1
	RAB29	ENST00000895155.1		c.*1219G>T		3_prime_UTR	Exon 6 of 6	ENSP00000565214.1
	RAB29	ENST00000895156.1		c.*1219G>T		3_prime_UTR	Exon 6 of 6	ENSP00000565215.1

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133269 AN: 152058 Hom.: 59527 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.885

GnomAD4 exome AF: 1.00 AC: 10 AN: 10 Hom.: 5 Cov.: 0 AF XY: 1.00 AC XY: 8 AN XY: 8

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 6 AN: 6

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.876 AC: 133353 AN: 152176 Hom.: 59553 Cov.: 32 AF XY: 0.876 AC XY: 65180 AN XY: 74424

African (AFR) AF: 0.697 AC: 28912 AN: 41458

American (AMR) AF: 0.880 AC: 13459 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3166 AN: 3472

East Asian (EAS) AF: 0.857 AC: 4432 AN: 5172

South Asian (SAS) AF: 0.893 AC: 4309 AN: 4828

European-Finnish (FIN) AF: 0.969 AC: 10282 AN: 10610

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65763 AN: 68028

Other (OTH) AF: 0.886 AC: 1871 AN: 2112

Alfa AF: 0.936 Hom.: 269498

Bravo AF: 0.860

Asia WGS AF: 0.865 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.81
PhyloP100		-0.074
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: rs823136; hg19: chr1-205738251;