9-135695189-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001101677.2(SOHLH1):c.736C>T(p.Pro246Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000872 in 1,604,882 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 (★). Synonymous variant affecting the same amino acid position (i.e. P246P) has been classified as Likely benign.
Frequency
Consequence
NM_001101677.2 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 |
---|---|---|---|---|---|---|---|
SOHLH1 | NM_001101677.2 | c.736C>T | p.Pro246Ser | missense_variant | 6/8 | ENST00000425225.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOHLH1 | ENST00000425225.2 | c.736C>T | p.Pro246Ser | missense_variant | 6/8 | 5 | NM_001101677.2 | A2 | |
SOHLH1 | ENST00000298466.9 | c.736C>T | p.Pro246Ser | missense_variant | 6/7 | 1 | P2 | ||
SOHLH1 | ENST00000673731.1 | c.94C>T | p.Pro32Ser | missense_variant | 2/5 | ||||
SOHLH1 | ENST00000674066.1 | n.2326C>T | non_coding_transcript_exon_variant | 9/11 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152258Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000437 AC: 1AN: 228978Hom.: 0 AF XY: 0.00000800 AC XY: 1AN XY: 124996
GnomAD4 exome AF: 0.00000895 AC: 13AN: 1452624Hom.: 0 Cov.: 37 AF XY: 0.0000111 AC XY: 8AN XY: 721736
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152258Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.736C>T (p.P246S) alteration is located in exon 6 (coding exon 6) of the SOHLH1 gene. This alteration results from a C to T substitution at nucleotide position 736, causing the proline (P) at amino acid position 246 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