7-76404384-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080744.2(SSC4D):c.56G>T(p.Gly19Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080744.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSC4D | NM_080744.2 | c.56G>T | p.Gly19Val | missense_variant | Exon 2 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.56G>T | p.Gly19Val | missense_variant | Exon 2 of 12 | XP_024302432.1 | ||
ZP3 | NM_007155.6 | c.-67+6587C>A | intron_variant | Intron 1 of 8 | NP_009086.4 | |||
SSC4D | XM_017011750.2 | c.-33+5030G>T | intron_variant | Intron 1 of 7 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251010Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135686
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461676Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727126
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.56G>T (p.G19V) alteration is located in exon 2 (coding exon 1) of the SSC4D gene. This alteration results from a G to T substitution at nucleotide position 56, causing the glycine (G) at amino acid position 19 to be replaced by a valine (V). 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