chr19-40472721-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020971.3(SPTBN4):c.100C>T(p.Arg34Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,608,710 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020971.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPTBN4 | ENST00000598249.6 | c.100C>T | p.Arg34Trp | missense_variant | Exon 2 of 36 | 1 | NM_020971.3 | ENSP00000469242.1 | ||
SPTBN4 | ENST00000352632.7 | c.100C>T | p.Arg34Trp | missense_variant | Exon 2 of 36 | 5 | ENSP00000263373.2 | |||
SPTBN4 | ENST00000595535.5 | c.100C>T | p.Arg34Trp | missense_variant | Exon 2 of 27 | 5 | ENSP00000470693.1 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 151892Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000836 AC: 2AN: 239288Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 130388
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1456818Hom.: 0 Cov.: 30 AF XY: 0.00000690 AC XY: 5AN XY: 724442
GnomAD4 genome AF: 0.0000724 AC: 11AN: 151892Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74164
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.100C>T (p.R34W) alteration is located in exon 2 (coding exon 1) of the SPTBN4 gene. This alteration results from a C to T substitution at nucleotide position 100, causing the arginine (R) at amino acid position 34 to be replaced by a tryptophan (W). 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