12-26231045-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000242729.7(SSPN):c.701C>T(p.Thr234Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,613,710 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
ENST00000242729.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSPN | NM_005086.5 | c.701C>T | p.Thr234Met | missense_variant | 3/3 | ENST00000242729.7 | NP_005077.2 | |
LOC101928554 | XR_007063250.1 | n.166-11883G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSPN | ENST00000242729.7 | c.701C>T | p.Thr234Met | missense_variant | 3/3 | 1 | NM_005086.5 | ENSP00000242729 | P1 | |
ENST00000540625.5 | n.257G>A | non_coding_transcript_exon_variant | 3/3 | 3 | ||||||
ITPR2-AS1 | ENST00000540392.1 | n.131-16268G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000361 AC: 55AN: 152156Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000104 AC: 26AN: 251096Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135706
GnomAD4 exome AF: 0.0000814 AC: 119AN: 1461436Hom.: 0 Cov.: 31 AF XY: 0.0000688 AC XY: 50AN XY: 726958
GnomAD4 genome AF: 0.000361 AC: 55AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2021 | The c.701C>T (p.T234M) alteration is located in exon 3 (coding exon 3) of the SSPN gene. This alteration results from a C to T substitution at nucleotide position 701, causing the threonine (T) at amino acid position 234 to be replaced by a methionine (M). 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