chr1-17603513-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018125.4(ARHGEF10L):c.355C>T(p.Arg119Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018125.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGEF10L | ENST00000361221.8 | c.355C>T | p.Arg119Trp | missense_variant | Exon 6 of 29 | 1 | NM_018125.4 | ENSP00000355060.3 | ||
ARHGEF10L | ENST00000375415.5 | c.355C>T | p.Arg119Trp | missense_variant | Exon 5 of 27 | 1 | ENSP00000364564.1 | |||
ARHGEF10L | ENST00000482892.1 | n.54C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 249960Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135088
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461106Hom.: 0 Cov.: 32 AF XY: 0.0000771 AC XY: 56AN XY: 726792
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.355C>T (p.R119W) alteration is located in exon 6 (coding exon 5) of the ARHGEF10L gene. This alteration results from a C to T substitution at nucleotide position 355, causing the arginine (R) at amino acid position 119 to be replaced by a tryptophan (W). 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