16-69260219-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006750.4(SNTB2):c.964G>A(p.Gly322Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,614,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006750.4 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 |
---|---|---|---|---|---|---|---|
SNTB2 | NM_006750.4 | c.964G>A | p.Gly322Ser | missense_variant | 3/7 | ENST00000336278.9 | |
SNTB2 | NR_172088.1 | n.1053G>A | non_coding_transcript_exon_variant | 4/8 | |||
SNTB2 | NR_172089.1 | n.954G>A | non_coding_transcript_exon_variant | 3/7 | |||
SNTB2 | NR_172090.1 | n.798-9924G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNTB2 | ENST00000336278.9 | c.964G>A | p.Gly322Ser | missense_variant | 3/7 | 1 | NM_006750.4 | P1 | |
SNTB2 | ENST00000467311.5 | c.795-9924G>A | intron_variant, NMD_transcript_variant | 1 | |||||
SNTB2 | ENST00000525632.5 | c.478+92G>A | intron_variant | 3 | |||||
SNTB2 | ENST00000528525.1 | n.368G>A | non_coding_transcript_exon_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251426Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135894
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461890Hom.: 0 Cov.: 33 AF XY: 0.0000371 AC XY: 27AN XY: 727246
GnomAD4 genome AF: 0.000236 AC: 36AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2022 | The c.964G>A (p.G322S) alteration is located in exon 3 (coding exon 3) of the SNTB2 gene. This alteration results from a G to A substitution at nucleotide position 964, causing the glycine (G) at amino acid position 322 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