chr12-108788896-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018984.4(SSH1):c.2242C>T(p.Pro748Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,614,074 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 Uncertain significance (★).
Frequency
Consequence
NM_018984.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SSH1 | NM_018984.4 | c.2242C>T | p.Pro748Ser | missense_variant | 15/15 | ENST00000326495.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSH1 | ENST00000326495.10 | c.2242C>T | p.Pro748Ser | missense_variant | 15/15 | 1 | NM_018984.4 | P2 | |
SSH1 | ENST00000546433.5 | c.*1235C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251090Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135866
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461882Hom.: 0 Cov.: 33 AF XY: 0.0000358 AC XY: 26AN XY: 727244
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.2242C>T (p.P748S) alteration is located in exon 15 (coding exon 15) of the SSH1 gene. This alteration results from a C to T substitution at nucleotide position 2242, causing the proline (P) at amino acid position 748 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