dbSNP rs7225527: RHOT1:c.359+19622A>G (chr17-32227931-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000580392.5(RHOT1):c.359+19622A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 963,584 control chromosomes in the GnomAD database, including 16,887 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 0.18 ( 2578 hom., cov: 29)

Exomes 𝑓: 0.18 ( 14309 hom. )

Consequence

RHOT1
ENST00000580392.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

Variant links:

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]

RHOT1 links:

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

UBL5P2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBL5P2		n.32227931A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
RHOT1	ENST00000580392.5 link	c.359+19622A>G	intron_variant	Intron 3 of 3	3	ENSP00000463532.1	J3QLG2
RHOT1	ENST00000584852.1 link	c.131+16693A>G	intron_variant	Intron 2 of 2	5	ENSP00000461992.1	J3KRG7
UBL5P2	ENST00000583788.1 link	n.178T>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
RHOT1	ENST00000582586.1 link	n.59-13864A>G	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27441

AN:

151632

Hom.:

2571

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.178

GnomAD4 exome

AF:

0.180

AC:

146036

AN:

811834

Hom.:

14309

Cov.:

AF XY:

0.184

AC XY:

79068

AN XY:

428730

show subpopulations

Gnomad4 AFR exome

AF:

0.177

Gnomad4 AMR exome

AF:

0.240

Gnomad4 ASJ exome

AF:

0.201

Gnomad4 EAS exome

AF:

0.216

Gnomad4 SAS exome

AF:

0.279

Gnomad4 FIN exome

AF:

0.142

Gnomad4 NFE exome

AF:

0.161

Gnomad4 OTH exome

AF:

0.183

GnomAD4 genome

AF:

0.181

AC:

27471

AN:

151750

Hom.:

2578

Cov.:

AF XY:

0.181

AC XY:

13382

AN XY:

74136

show subpopulations

Gnomad4 AFR

AF:

0.183

Gnomad4 AMR

AF:

0.185

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.223

Gnomad4 SAS

AF:

0.273

Gnomad4 FIN

AF:

0.138

Gnomad4 NFE

AF:

0.175

Gnomad4 OTH

AF:

0.183

Alfa

AF:

0.179

Hom.:

305

Bravo

AF:

0.184

Asia WGS

AF:

0.274

AC:

953

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

2.3

DANN

Benign

0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over