7-76404361-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_080744.2(SSC4D):c.79G>A(p.Ala27Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_080744.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSC4D | NM_080744.2 | c.79G>A | p.Ala27Thr | missense_variant | Exon 2 of 11 | ENST00000275560.4 | NP_542782.1 | |
SSC4D | XM_024446664.2 | c.79G>A | p.Ala27Thr | missense_variant | Exon 2 of 12 | XP_024302432.1 | ||
ZP3 | NM_007155.6 | c.-67+6564C>T | intron_variant | Intron 1 of 8 | NP_009086.4 | |||
SSC4D | XM_017011750.2 | c.-33+5053G>A | intron_variant | Intron 1 of 7 | XP_016867239.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250080Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135184
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461072Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726826
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at