8-120632616-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_021021.4(SNTB1):c.824C>T(p.Thr275Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000483 in 1,614,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T275R) has been classified as Uncertain significance.
Frequency
Consequence
NM_021021.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNTB1 | NM_021021.4 | c.824C>T | p.Thr275Met | missense_variant | 3/7 | ENST00000517992.2 | |
SNTB1 | XM_011517239.3 | c.824C>T | p.Thr275Met | missense_variant | 3/5 | ||
SNTB1 | XM_047422126.1 | c.245C>T | p.Thr82Met | missense_variant | 3/7 | ||
SNTB1 | XM_047422127.1 | c.245C>T | p.Thr82Met | missense_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNTB1 | ENST00000517992.2 | c.824C>T | p.Thr275Met | missense_variant | 3/7 | 1 | NM_021021.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251396Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135882
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 727236
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.824C>T (p.T275M) alteration is located in exon 3 (coding exon 3) of the SNTB1 gene. This alteration results from a C to T substitution at nucleotide position 824, causing the threonine (T) at amino acid position 275 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