chr6-166320236-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145169.3(SFT2D1):c.461G>A(p.Cys154Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,459,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145169.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFT2D1 | NM_145169.3 | c.461G>A | p.Cys154Tyr | missense_variant | Exon 8 of 8 | ENST00000361731.4 | NP_660152.1 | |
SFT2D1 | NR_130112.2 | n.548G>A | non_coding_transcript_exon_variant | Exon 9 of 9 | ||||
SFT2D1 | NR_130113.2 | n.453G>A | non_coding_transcript_exon_variant | Exon 7 of 7 | ||||
SFT2D1 | NR_130114.2 | n.444G>A | non_coding_transcript_exon_variant | Exon 7 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFT2D1 | ENST00000361731.4 | c.461G>A | p.Cys154Tyr | missense_variant | Exon 8 of 8 | 1 | NM_145169.3 | ENSP00000354590.3 | ||
SFT2D1 | ENST00000479490.1 | n.1853G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 1 | |||||
SFT2D1 | ENST00000487841.5 | n.2200G>A | non_coding_transcript_exon_variant | Exon 8 of 8 | 1 | |||||
SFT2D1 | ENST00000478705.5 | n.579G>A | non_coding_transcript_exon_variant | Exon 9 of 9 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459366Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 725918
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.461G>A (p.C154Y) alteration is located in exon 8 (coding exon 8) of the SFT2D1 gene. This alteration results from a G to A substitution at nucleotide position 461, causing the cysteine (C) at amino acid position 154 to be replaced by a tyrosine (Y). 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