rs900318

Variant names:

• chr3-129102964-G-A
• rs900318
• NM_198490.3:c.205-7795C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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:42969): (ISY1-RAB43 readthrough) This locus represents naturally occurring read-through transcription between the neighboring ISY1 (ISY1 splicing factor homolog) and RAB43 (RAB43, member RAS oncogene family) gene on chromosome 3. The read-through transcript encodes a protein that shares sequence identity with the upstream gene product, but its C-terminus is distinct due to a frameshift relative to the downstream gene. [provided by RefSeq, Mar 2011]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198490.3. 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
	RAB43	NM_198490.3	MANE Select	c.205-7795C>T		intron	N/A	NP_940892.1	Q86YS6-1
	ISY1-RAB43	NM_001204890.2		c.852-7795C>T		intron	N/A	NP_001191819.1
	RAB43	NM_001204883.2		c.205-7795C>T		intron	N/A	NP_001191812.1	Q86YS6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB43	ENST00000315150.10	TSL:1 MANE Select	c.205-7795C>T		intron	N/A	ENSP00000319781.6	Q86YS6-1
	ISY1-RAB43	ENST00000418265.1	TSL:2	c.852-7795C>T		intron	N/A	ENSP00000411822.1
	RAB43	ENST00000915979.1		c.262-7795C>T		intron	N/A	ENSP00000586038.1

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

African (AFR) AF: 0.688 AC: 28545 AN: 41462

American (AMR) AF: 0.905 AC: 13843 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3341 AN: 3472

East Asian (EAS) AF: 0.885 AC: 4580 AN: 5174

South Asian (SAS) AF: 0.846 AC: 4084 AN: 4826

European-Finnish (FIN) AF: 0.955 AC: 10128 AN: 10610

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66253 AN: 68024

Other (OTH) AF: 0.898 AC: 1899 AN: 2114

Alfa AF: 0.927 Hom.: 14568

Bravo AF: 0.868

Asia WGS AF: 0.844 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.5
DANN	Benign	0.92
PhyloP100		-0.47
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: rs900318; hg19: chr3-128821807;