7-76390345-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080744.2(SSC4D):c.1442G>A(p.Arg481Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,602,496 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 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.1442G>A | p.Arg481Gln | missense_variant | Exon 11 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.1529G>A | p.Arg510Gln | missense_variant | Exon 12 of 12 | XP_024302432.1 | ||
SSC4D | XM_017011750.2 | c.935G>A | p.Arg312Gln | missense_variant | Exon 8 of 8 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000168 AC: 4AN: 238616Hom.: 0 AF XY: 0.0000311 AC XY: 4AN XY: 128786
GnomAD4 exome AF: 0.0000145 AC: 21AN: 1450342Hom.: 1 Cov.: 31 AF XY: 0.00000833 AC XY: 6AN XY: 720224
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1442G>A (p.R481Q) alteration is located in exon 11 (coding exon 10) of the SSC4D gene. This alteration results from a G to A substitution at nucleotide position 1442, causing the arginine (R) at amino acid position 481 to be replaced by a glutamine (Q). 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