chr19-4283154-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020209.4(SHD):c.504C>G(p.Ser168Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,614,032 control chromosomes in the GnomAD database, including 1 homozygotes. 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. S168N) 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHD | ENST00000543264.7 | c.504C>G | p.Ser168Arg | missense_variant | Exon 3 of 6 | 1 | NM_020209.4 | ENSP00000446058.1 | ||
SHD | ENST00000599689.1 | c.504C>G | p.Ser168Arg | missense_variant | Exon 3 of 5 | 5 | ENSP00000470181.1 | |||
SHD | ENST00000593383.1 | n.72C>G | non_coding_transcript_exon_variant | Exon 1 of 4 | 3 | ENSP00000472139.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250390Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135448
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461866Hom.: 1 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727230
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152166Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.504C>G (p.S168R) alteration is located in exon 3 (coding exon 3) of the SHD gene. This alteration results from a C to G substitution at nucleotide position 504, causing the serine (S) at amino acid position 168 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