7-76404386-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080744.2(SSC4D):āc.54G>Cā(p.Trp18Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,976 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_080744.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSC4D | NM_080744.2 | c.54G>C | p.Trp18Cys | missense_variant | Exon 2 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.54G>C | p.Trp18Cys | missense_variant | Exon 2 of 12 | XP_024302432.1 | ||
ZP3 | NM_007155.6 | c.-67+6589C>G | intron_variant | Intron 1 of 8 | NP_009086.4 | |||
SSC4D | XM_017011750.2 | c.-33+5028G>C | intron_variant | Intron 1 of 7 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152160Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000996 AC: 25AN: 251060Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135688
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461698Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727138
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152278Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.54G>C (p.W18C) alteration is located in exon 2 (coding exon 1) of the SSC4D gene. This alteration results from a G to C substitution at nucleotide position 54, causing the tryptophan (W) at amino acid position 18 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