chr19-4280217-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020209.4(SHD):c.154C>T(p.Arg52Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R52L) has been classified as Uncertain significance.
Frequency
Consequence
NM_020209.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152140Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000565 AC: 14AN: 247718Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134760
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461642Hom.: 0 Cov.: 33 AF XY: 0.0000316 AC XY: 23AN XY: 727128
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152140Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.154C>T (p.R52C) alteration is located in exon 1 (coding exon 1) of the SHD gene. This alteration results from a C to T substitution at nucleotide position 154, causing the arginine (R) at amino acid position 52 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