2-85344034-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017750.4(RETSAT):c.1498G>A(p.Val500Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,614,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017750.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RETSAT | ENST00000295802.9 | c.1498G>A | p.Val500Met | missense_variant | Exon 9 of 11 | 1 | NM_017750.4 | ENSP00000295802.4 | ||
RETSAT | ENST00000429806.5 | n.880+205G>A | intron_variant | Intron 6 of 7 | 1 | ENSP00000388202.1 | ||||
RETSAT | ENST00000449375.1 | c.862G>A | p.Val288Met | missense_variant | Exon 6 of 8 | 5 | ENSP00000412166.1 | |||
RETSAT | ENST00000438611.4 | n.*508+205G>A | intron_variant | Intron 4 of 5 | 5 | ENSP00000444814.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251430Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135880
GnomAD4 exome AF: 0.0000609 AC: 89AN: 1461870Hom.: 0 Cov.: 34 AF XY: 0.0000908 AC XY: 66AN XY: 727244
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1498G>A (p.V500M) alteration is located in exon 9 (coding exon 9) of the RETSAT gene. This alteration results from a G to A substitution at nucleotide position 1498, causing the valine (V) at amino acid position 500 to be replaced by a methionine (M). 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