7-76390253-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_080744.2(SSC4D):c.1534C>T(p.Arg512Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,896 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSC4D | NM_080744.2 | c.1534C>T | p.Arg512Cys | missense_variant | Exon 11 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.1621C>T | p.Arg541Cys | missense_variant | Exon 12 of 12 | XP_024302432.1 | ||
SSC4D | XM_017011750.2 | c.1027C>T | p.Arg343Cys | missense_variant | Exon 8 of 8 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250438Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135466
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461644Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727146
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1534C>T (p.R512C) alteration is located in exon 11 (coding exon 10) of the SSC4D gene. This alteration results from a C to T substitution at nucleotide position 1534, causing the arginine (R) at amino acid position 512 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