7-76391990-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080744.2(SSC4D):c.1385G>T(p.Arg462Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 1,442,074 control chromosomes in the GnomAD database, including 1 homozygotes. 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.1385G>T | p.Arg462Leu | missense_variant | Exon 10 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.1472G>T | p.Arg491Leu | missense_variant | Exon 11 of 12 | XP_024302432.1 | ||
SSC4D | XM_017011750.2 | c.878G>T | p.Arg293Leu | missense_variant | Exon 7 of 8 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000603 AC: 13AN: 215550Hom.: 0 AF XY: 0.0000259 AC XY: 3AN XY: 115950
GnomAD4 exome AF: 0.0000125 AC: 18AN: 1442074Hom.: 1 Cov.: 31 AF XY: 0.00000419 AC XY: 3AN XY: 715278
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1385G>T (p.R462L) alteration is located in exon 10 (coding exon 9) of the SSC4D gene. This alteration results from a G to T substitution at nucleotide position 1385, causing the arginine (R) at amino acid position 462 to be replaced by a leucine (L). 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