ENST00000580392.5:c.359+19622A>G

Variant names:

• chr17-32227930-T-G
• ENST00000580392.5:c.359+19621T>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000580392.5(RHOT1):​c.359+19621T>G 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: 29)
• Consequence: RHOT1 ENST00000580392.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

RHOT1 (HGNC:21168): (ras homolog family member T1) Predicted to enable GTP binding activity and GTPase activity. Involved in cellular homeostasis; mitochondrial outer membrane permeabilization; and mitochondrion transport along microtubule. Is integral component of mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

UBL5P2 (HGNC:44640): (ubiquitin like 5 pseudogene 2)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBL5P2		n.32227930T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RHOT1	ENST00000580392.5	c.359+19621T>G		intron_variant	Intron 3 of 3	3		ENSP00000463532.1
RHOT1	ENST00000584852.1	c.131+16692T>G		intron_variant	Intron 2 of 2	5		ENSP00000461992.1
UBL5P2	ENST00000583788.1	n.179A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
RHOT1	ENST00000582586.1	n.59-13865T>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 11

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	2.7
DANN	Benign	0.86

Splicing

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: chr17-30554949;