7-76393715-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080744.2(SSC4D):āc.1023T>Gā(p.Ser341Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000255 in 1,386,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_080744.2 missense, splice_region
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.1023T>G | p.Ser341Arg | missense_variant, splice_region_variant | Exon 9 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.1110T>G | p.Ser370Arg | missense_variant, splice_region_variant | Exon 10 of 12 | XP_024302432.1 | ||
SSC4D | XM_017011750.2 | c.516T>G | p.Ser172Arg | missense_variant, splice_region_variant | Exon 6 of 8 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151848Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000624 AC: 1AN: 16020Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 9314
GnomAD4 exome AF: 0.000282 AC: 348AN: 1235034Hom.: 0 Cov.: 41 AF XY: 0.000266 AC XY: 160AN XY: 602484
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151848Hom.: 0 Cov.: 34 AF XY: 0.0000270 AC XY: 2AN XY: 74172
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1023T>G (p.S341R) alteration is located in exon 9 (coding exon 8) of the SSC4D gene. This alteration results from a T to G substitution at nucleotide position 1023, causing the serine (S) at amino acid position 341 to be replaced by an arginine (R). 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