chr16-81999140-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_145168.3(SDR42E1):c.1153C>A(p.Leu385Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,613,916 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDR42E1 | NM_145168.3 | c.1153C>A | p.Leu385Met | missense_variant | 3/3 | ENST00000328945.7 | |
SDR42E1 | XM_005256257.5 | c.1153C>A | p.Leu385Met | missense_variant | 4/4 | ||
SDR42E1 | XM_011523471.4 | c.1144C>A | p.Leu382Met | missense_variant | 3/3 | ||
SDR42E1 | XM_047434925.1 | c.1144C>A | p.Leu382Met | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDR42E1 | ENST00000328945.7 | c.1153C>A | p.Leu385Met | missense_variant | 3/3 | 1 | NM_145168.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000920 AC: 140AN: 152192Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000742 AC: 185AN: 249186Hom.: 0 AF XY: 0.000725 AC XY: 98AN XY: 135194
GnomAD4 exome AF: 0.00146 AC: 2131AN: 1461724Hom.: 3 Cov.: 31 AF XY: 0.00135 AC XY: 984AN XY: 727146
GnomAD4 genome AF: 0.000920 AC: 140AN: 152192Hom.: 2 Cov.: 32 AF XY: 0.000888 AC XY: 66AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 19, 2021 | The c.1153C>A (p.L385M) alteration is located in exon 3 (coding exon 2) of the SDR42E1 gene. This alteration results from a C to A substitution at nucleotide position 1153, causing the leucine (L) at amino acid position 385 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