7-76400439-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_080744.2(SSC4D):c.322C>T(p.Pro108Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000142 in 1,607,102 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 (★).
Frequency
Consequence
NM_080744.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSC4D | NM_080744.2 | c.322C>T | p.Pro108Ser | missense_variant | Exon 4 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.409C>T | p.Pro137Ser | missense_variant | Exon 5 of 12 | XP_024302432.1 | ||
ZP3 | NM_007155.6 | c.-67+2642G>A | intron_variant | Intron 1 of 8 | NP_009086.4 | |||
SSC4D | XM_017011750.2 | c.-32-1642C>T | intron_variant | Intron 1 of 7 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000583 AC: 14AN: 240060Hom.: 0 AF XY: 0.0000686 AC XY: 9AN XY: 131272
GnomAD4 exome AF: 0.000151 AC: 220AN: 1454846Hom.: 0 Cov.: 33 AF XY: 0.000149 AC XY: 108AN XY: 723108
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.322C>T (p.P108S) alteration is located in exon 4 (coding exon 3) of the SSC4D gene. This alteration results from a C to T substitution at nucleotide position 322, causing the proline (P) at amino acid position 108 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