NM_032740.4:c.179C>T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032740.4(SFT2D3):c.179C>T(p.Ser60Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000407 in 1,327,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032740.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFT2D3 | NM_032740.4 | c.179C>T | p.Ser60Leu | missense_variant | Exon 1 of 1 | ENST00000310981.6 | NP_116129.3 | |
WDR33 | NM_018383.5 | c.*4616G>A | 3_prime_UTR_variant | Exon 22 of 22 | ENST00000322313.9 | NP_060853.3 | ||
WDR33 | XM_011511436.2 | c.*4616G>A | 3_prime_UTR_variant | Exon 22 of 22 | XP_011509738.1 | |||
WDR33 | XM_005263697.4 | c.*4786G>A | 3_prime_UTR_variant | Exon 21 of 21 | XP_005263754.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFT2D3 | ENST00000310981.6 | c.179C>T | p.Ser60Leu | missense_variant | Exon 1 of 1 | 6 | NM_032740.4 | ENSP00000310803.3 | ||
WDR33 | ENST00000322313.9 | c.*4616G>A | 3_prime_UTR_variant | Exon 22 of 22 | 1 | NM_018383.5 | ENSP00000325377.3 | |||
ENSG00000293688 | ENST00000718293.1 | n.-247G>A | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0000397 AC: 6AN: 151164Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000732 AC: 1AN: 13670 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.0000408 AC: 48AN: 1175862Hom.: 0 Cov.: 31 AF XY: 0.0000489 AC XY: 28AN XY: 573148 show subpopulations
GnomAD4 genome AF: 0.0000397 AC: 6AN: 151164Hom.: 0 Cov.: 33 AF XY: 0.0000271 AC XY: 2AN XY: 73808 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.179C>T (p.S60L) alteration is located in exon 1 (coding exon 1) of the SFT2D3 gene. This alteration results from a C to T substitution at nucleotide position 179, causing the serine (S) at amino acid position 60 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