chr12-56923865-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_148897.3(SDR9C7):c.910C>T(p.Arg304Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000231 in 1,613,262 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_148897.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000108 AC: 27AN: 250408Hom.: 0 AF XY: 0.0000961 AC XY: 13AN XY: 135272
GnomAD4 exome AF: 0.000237 AC: 347AN: 1461108Hom.: 0 Cov.: 31 AF XY: 0.000224 AC XY: 163AN XY: 726804
GnomAD4 genome AF: 0.000164 AC: 25AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74336
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.910C>T (p.R304W) alteration is located in exon 4 (coding exon 4) of the SDR9C7 gene. This alteration results from a C to T substitution at nucleotide position 910, causing the arginine (R) at amino acid position 304 to be replaced by a tryptophan (W). 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