rs34897

Variant names:

• chr5-95750599-T-A
• NM_014899.4:c.571-1640T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-95750599-T-A
• chr5-95750599-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014899.4(RHOBTB3):​c.571-1640T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: RHOBTB3 NM_014899.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

Genes affected

RHOBTB3 (HGNC:18757): (Rho related BTB domain containing 3) Enables ATP binding activity and small GTPase binding activity. Involved in retrograde transport, endosome to Golgi. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RHOBTB3	NM_014899.4	c.571-1640T>A		intron_variant	Intron 4 of 11	ENST00000379982.8	NP_055714.3
RHOBTB3	XM_011543279.3	c.571-1640T>A		intron_variant	Intron 4 of 10		XP_011541581.1
RHOBTB3	XM_017009237.2	c.-12-1640T>A		intron_variant	Intron 4 of 11		XP_016864726.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RHOBTB3	ENST00000379982.8	c.571-1640T>A		intron_variant	Intron 4 of 11	1	NM_014899.4	ENSP00000369318.3
RHOBTB3	ENST00000502541.1	n.291+2112T>A		intron_variant	Intron 2 of 3	5		ENSP00000421875.1
RHOBTB3	ENST00000504949.1	n.702-1640T>A		intron_variant	Intron 4 of 5	2
RHOBTB3	ENST00000510623.1	n.*66-1640T>A		intron_variant	Intron 2 of 2	2		ENSP00000423652.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.68

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-95086303;