chr12-56929431-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_148897.3(SDR9C7):āc.683A>Gā(p.Gln228Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000713 in 1,613,038 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 (ā ).
Frequency
Consequence
NM_148897.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDR9C7 | NM_148897.3 | c.683A>G | p.Gln228Arg | missense_variant | 3/4 | ENST00000293502.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDR9C7 | ENST00000293502.2 | c.683A>G | p.Gln228Arg | missense_variant | 3/4 | 1 | NM_148897.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000187 AC: 47AN: 251342Hom.: 1 AF XY: 0.000184 AC XY: 25AN XY: 135832
GnomAD4 exome AF: 0.0000691 AC: 101AN: 1460828Hom.: 1 Cov.: 31 AF XY: 0.0000730 AC XY: 53AN XY: 726450
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74372
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.683A>G (p.Q228R) alteration is located in exon 3 (coding exon 3) of the SDR9C7 gene. This alteration results from a A to G substitution at nucleotide position 683, causing the glutamine (Q) at amino acid position 228 to be replaced by an arginine (R). 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