rs900318

Positions:

• chr3-129102964-G-A
• chr3-129102964-G-C
• chr3-129102964-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198490.3(RAB43):​c.205-7795C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,180 control chromosomes in the GnomAD database, including 59,980 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 (59980 hom., cov: 33)
• Consequence: RAB43 NM_198490.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471

Genes affected

RAB43 (HGNC:19983): (RAB43, member RAS oncogene family) Enables GTPase activity. Involved in several processes, including Golgi organization; phagosome maturation; and retrograde transport, plasma membrane to Golgi. Located in Golgi apparatus and phagocytic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ISY1-RAB43 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB43	NM_198490.3	c.205-7795C>T		intron_variant		ENST00000315150.10	NP_940892.1
ISY1-RAB43	NM_001204890.2	c.852-7795C>T		intron_variant			NP_001191819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB43	ENST00000315150.10	c.205-7795C>T		intron_variant		1	NM_198490.3	ENSP00000319781	P1

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133810 AN: 152062 Hom.: 59975 Cov.: 33

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.902

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.880 AC: 133846 AN: 152180 Hom.: 59980 Cov.: 33 AF XY: 0.879 AC XY: 65401 AN XY: 74402

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.898

Alfa AF: 0.933 Hom.: 14375

Bravo AF: 0.868

Asia WGS AF: 0.844 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.5
DANN	Benign	0.92

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

Publications

LitVar

Other links and lift over

dbSNP: rs900318; hg19: chr3-128821807;