7-76395259-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080744.2(SSC4D):c.940C>T(p.Pro314Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,613,838 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 (★).
Frequency
Consequence
NM_080744.2 missense
Scores
Clinical Significance
Conservation
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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.940C>T | p.Pro314Ser | missense_variant | Exon 7 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.1027C>T | p.Pro343Ser | missense_variant | Exon 8 of 12 | XP_024302432.1 | ||
SSC4D | XM_017011750.2 | c.433C>T | p.Pro145Ser | missense_variant | Exon 4 of 8 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251392Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135876
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461524Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727050
GnomAD4 genome AF: 0.000282 AC: 43AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.940C>T (p.P314S) alteration is located in exon 7 (coding exon 6) of the SSC4D gene. This alteration results from a C to T substitution at nucleotide position 940, causing the proline (P) at amino acid position 314 to be replaced by a serine (S). 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