chr17-32209372-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000358365.7(RHOT1):c.1762C>T(p.Leu588Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,609,672 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000358365.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHOT1 | NM_001033566.3 | c.1739+1063C>T | intron_variant | ENST00000545287.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHOT1 | ENST00000545287.7 | c.1739+1063C>T | intron_variant | 5 | NM_001033566.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000196 AC: 49AN: 250394Hom.: 1 AF XY: 0.000259 AC XY: 35AN XY: 135336
GnomAD4 exome AF: 0.000160 AC: 233AN: 1457420Hom.: 1 Cov.: 28 AF XY: 0.000190 AC XY: 138AN XY: 725170
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2022 | The c.1762C>T (p.L588F) alteration is located in exon 19 (coding exon 19) of the RHOT1 gene. This alteration results from a C to T substitution at nucleotide position 1762, causing the leucine (L) at amino acid position 588 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at