16-82000043-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_145168.3(SDR42E1):c.250A>G(p.Met84Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,614,190 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145168.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDR42E1 | NM_145168.3 | c.250A>G | p.Met84Val | missense_variant | 3/3 | ENST00000328945.7 | |
SDR42E1 | XM_005256257.5 | c.250A>G | p.Met84Val | missense_variant | 4/4 | ||
SDR42E1 | XM_011523471.4 | c.241A>G | p.Met81Val | missense_variant | 3/3 | ||
SDR42E1 | XM_047434925.1 | c.241A>G | p.Met81Val | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDR42E1 | ENST00000328945.7 | c.250A>G | p.Met84Val | missense_variant | 3/3 | 1 | NM_145168.3 | P1 | |
SDR42E1 | ENST00000532128.5 | c.241A>G | p.Met81Val | missense_variant | 4/4 | 5 | |||
SDR42E1 | ENST00000534209.1 | n.583A>G | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461884Hom.: 1 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727240
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.250A>G (p.M84V) alteration is located in exon 3 (coding exon 2) of the SDR42E1 gene. This alteration results from a A to G substitution at nucleotide position 250, causing the methionine (M) at amino acid position 84 to be replaced by a valine (V). 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
Publications
No publications associated with this variant yet.