chr15-78991760-T-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001145648.3(RASGRF1):c.3062A>T(p.His1021Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,613,742 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145648.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASGRF1 | NM_001145648.3 | c.3062A>T | p.His1021Leu | missense_variant | 21/27 | ENST00000558480.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASGRF1 | ENST00000558480.7 | c.3062A>T | p.His1021Leu | missense_variant | 21/27 | 2 | NM_001145648.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251366Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135866
GnomAD4 exome AF: 0.000108 AC: 158AN: 1461724Hom.: 1 Cov.: 31 AF XY: 0.000117 AC XY: 85AN XY: 727170
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.3110A>T (p.H1037L) alteration is located in exon 22 (coding exon 22) of the RASGRF1 gene. This alteration results from a A to T substitution at nucleotide position 3110, causing the histidine (H) at amino acid position 1037 to be replaced by a leucine (L). 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