chr7-76404377-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080744.2(SSC4D):c.63G>T(p.Arg21Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,742 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSC4D | NM_080744.2 | c.63G>T | p.Arg21Ser | missense_variant | Exon 2 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.63G>T | p.Arg21Ser | missense_variant | Exon 2 of 12 | XP_024302432.1 | ||
ZP3 | NM_007155.6 | c.-67+6580C>A | intron_variant | Intron 1 of 8 | NP_009086.4 | |||
SSC4D | XM_017011750.2 | c.-33+5037G>T | intron_variant | Intron 1 of 7 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250932Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135630
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461588Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727094
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.63G>T (p.R21S) alteration is located in exon 2 (coding exon 1) of the SSC4D gene. This alteration results from a G to T substitution at nucleotide position 63, causing the arginine (R) at amino acid position 21 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