16-82000018-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145168.3(SDR42E1):c.275G>A(p.Arg92Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDR42E1 | NM_145168.3 | c.275G>A | p.Arg92Gln | missense_variant | 3/3 | ENST00000328945.7 | |
SDR42E1 | XM_005256257.5 | c.275G>A | p.Arg92Gln | missense_variant | 4/4 | ||
SDR42E1 | XM_011523471.4 | c.266G>A | p.Arg89Gln | missense_variant | 3/3 | ||
SDR42E1 | XM_047434925.1 | c.266G>A | p.Arg89Gln | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDR42E1 | ENST00000328945.7 | c.275G>A | p.Arg92Gln | missense_variant | 3/3 | 1 | NM_145168.3 | P1 | |
SDR42E1 | ENST00000532128.5 | c.266G>A | p.Arg89Gln | missense_variant | 4/4 | 5 | |||
SDR42E1 | ENST00000534209.1 | n.608G>A | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 41AN: 249546Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135386
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727240
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2021 | The c.275G>A (p.R92Q) alteration is located in exon 3 (coding exon 2) of the SDR42E1 gene. This alteration results from a G to A substitution at nucleotide position 275, causing the arginine (R) at amino acid position 92 to be replaced by a glutamine (Q). 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