NM_148897.3:c.718C>T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_148897.3(SDR9C7):c.718C>T(p.Arg240Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000309 in 1,597,288 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_148897.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00122 AC: 186AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000458 AC: 115AN: 251126Hom.: 0 AF XY: 0.000442 AC XY: 60AN XY: 135728
GnomAD4 exome AF: 0.000213 AC: 308AN: 1445078Hom.: 1 Cov.: 31 AF XY: 0.000220 AC XY: 157AN XY: 714582
GnomAD4 genome AF: 0.00122 AC: 186AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.00117 AC XY: 87AN XY: 74424
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function -
Inborn genetic diseases Uncertain:1
The c.718C>T (p.R240C) alteration is located in exon 3 (coding exon 3) of the SDR9C7 gene. This alteration results from a C to T substitution at nucleotide position 718, causing the arginine (R) at amino acid position 240 to be replaced by a cysteine (C). 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