NM_006750.4:c.416C>T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_006750.4(SNTB2):c.416C>T(p.Pro139Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000847 in 1,534,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNTB2 | NM_006750.4 | c.416C>T | p.Pro139Leu | missense_variant | Exon 1 of 7 | ENST00000336278.9 | NP_006741.1 | |
SNTB2 | NR_172088.1 | n.419C>T | non_coding_transcript_exon_variant | Exon 1 of 8 | ||||
SNTB2 | NR_172089.1 | n.419C>T | non_coding_transcript_exon_variant | Exon 1 of 7 | ||||
SNTB2 | NR_172090.1 | n.419C>T | non_coding_transcript_exon_variant | Exon 1 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000397 AC: 6AN: 151120Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000506 AC: 7AN: 1383686Hom.: 0 Cov.: 31 AF XY: 0.00000438 AC XY: 3AN XY: 684914
GnomAD4 genome AF: 0.0000397 AC: 6AN: 151120Hom.: 0 Cov.: 31 AF XY: 0.0000271 AC XY: 2AN XY: 73800
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.416C>T (p.P139L) alteration is located in exon 1 (coding exon 1) of the SNTB2 gene. This alteration results from a C to T substitution at nucleotide position 416, causing the proline (P) at amino acid position 139 to be replaced by a leucine (L). 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