rs778228977
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019605.5(SERTAD4):c.652T>C(p.Ser218Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019605.5 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 |
---|---|---|---|---|---|---|---|---|
SERTAD4 | NM_019605.5 | c.652T>C | p.Ser218Pro | missense_variant | Exon 4 of 4 | ENST00000367012.4 | NP_062551.1 | |
SERTAD4 | NM_001375428.1 | c.652T>C | p.Ser218Pro | missense_variant | Exon 4 of 4 | NP_001362357.1 | ||
SERTAD4 | NM_001354173.2 | c.291+2310T>C | intron_variant | Intron 3 of 4 | NP_001341102.1 | |||
SERTAD4 | XM_047425536.1 | c.291+2310T>C | intron_variant | Intron 3 of 4 | XP_047281492.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERTAD4 | ENST00000367012.4 | c.652T>C | p.Ser218Pro | missense_variant | Exon 4 of 4 | 1 | NM_019605.5 | ENSP00000355979.3 | ||
SERTAD4 | ENST00000490620.5 | n.856T>C | non_coding_transcript_exon_variant | Exon 4 of 4 | 4 | |||||
SERTAD4 | ENST00000482421.1 | n.309+2310T>C | intron_variant | Intron 2 of 3 | 3 | |||||
SERTAD4 | ENST00000483884.1 | n.158+3783T>C | intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250392Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135454
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461860Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 727238
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.652T>C (p.S218P) alteration is located in exon 4 (coding exon 3) of the SERTAD4 gene. This alteration results from a T to C substitution at nucleotide position 652, causing the serine (S) at amino acid position 218 to be replaced by a proline (P). 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