chr19-40472632-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020971.3(SPTBN4):āc.11T>Cā(p.Val4Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,613,040 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 (ā ).
Frequency
Consequence
NM_020971.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTBN4 | NM_020971.3 | c.11T>C | p.Val4Ala | missense_variant | 2/36 | ENST00000598249.6 | |
SPTBN4 | XM_017027049.2 | c.11T>C | p.Val4Ala | missense_variant | 2/36 | ||
SPTBN4 | XM_017027051.2 | c.11T>C | p.Val4Ala | missense_variant | 2/31 | ||
SPTBN4 | XM_017027052.2 | c.11T>C | p.Val4Ala | missense_variant | 2/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN4 | ENST00000598249.6 | c.11T>C | p.Val4Ala | missense_variant | 2/36 | 1 | NM_020971.3 | P1 | |
SPTBN4 | ENST00000352632.7 | c.11T>C | p.Val4Ala | missense_variant | 2/36 | 5 | P1 | ||
SPTBN4 | ENST00000595535.5 | c.11T>C | p.Val4Ala | missense_variant | 2/27 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152198Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000846 AC: 21AN: 248348Hom.: 0 AF XY: 0.0000817 AC XY: 11AN XY: 134592
GnomAD4 exome AF: 0.000117 AC: 171AN: 1460724Hom.: 0 Cov.: 30 AF XY: 0.000111 AC XY: 81AN XY: 726508
GnomAD4 genome AF: 0.000164 AC: 25AN: 152316Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74478
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.11T>C (p.V4A) alteration is located in exon 2 (coding exon 1) of the SPTBN4 gene. This alteration results from a T to C substitution at nucleotide position 11, causing the valine (V) at amino acid position 4 to be replaced by an alanine (A). 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