chr22-24313359-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP5BP4BS2
The NM_015330.6(SPECC1L):c.200C>T(p.Thr67Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000254 in 1,613,918 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_015330.6 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 |
---|---|---|---|---|---|---|---|---|
SPECC1L | NM_015330.6 | c.200C>T | p.Thr67Met | missense_variant | Exon 4 of 17 | ENST00000314328.14 | NP_056145.5 | |
SPECC1L | NM_001145468.4 | c.200C>T | p.Thr67Met | missense_variant | Exon 3 of 16 | NP_001138940.4 | ||
SPECC1L | NM_001254732.3 | c.200C>T | p.Thr67Met | missense_variant | Exon 3 of 15 | NP_001241661.3 | ||
SPECC1L-ADORA2A | NR_103546.1 | n.508C>T | non_coding_transcript_exon_variant | Exon 4 of 20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPECC1L | ENST00000314328.14 | c.200C>T | p.Thr67Met | missense_variant | Exon 4 of 17 | 1 | NM_015330.6 | ENSP00000325785.8 | ||
SPECC1L-ADORA2A | ENST00000358654.2 | n.200C>T | non_coding_transcript_exon_variant | Exon 4 of 20 | 2 | ENSP00000351480.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251476Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135912
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461864Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727230
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
Teebi hypertelorism syndrome 1 Pathogenic:1
Variant confirmed as disease-causing by referring clinical team -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at