chr8-120693795-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021021.4(SNTB1):c.685C>T(p.Pro229Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021021.4 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 |
---|---|---|---|---|---|---|---|
SNTB1 | NM_021021.4 | c.685C>T | p.Pro229Ser | missense_variant | 2/7 | ENST00000517992.2 | |
SNTB1 | XM_011517239.3 | c.685C>T | p.Pro229Ser | missense_variant | 2/5 | ||
SNTB1 | XM_047422126.1 | c.106C>T | p.Pro36Ser | missense_variant | 2/7 | ||
SNTB1 | XM_047422127.1 | c.106C>T | p.Pro36Ser | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNTB1 | ENST00000517992.2 | c.685C>T | p.Pro229Ser | missense_variant | 2/7 | 1 | NM_021021.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251348Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135830
GnomAD4 exome AF: 0.0000705 AC: 103AN: 1461826Hom.: 0 Cov.: 31 AF XY: 0.0000729 AC XY: 53AN XY: 727206
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.685C>T (p.P229S) alteration is located in exon 2 (coding exon 2) of the SNTB1 gene. This alteration results from a C to T substitution at nucleotide position 685, causing the proline (P) at amino acid position 229 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