chr19-49651236-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021228.3(SCAF1):c.847G>T(p.Asp283Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D283E) has been classified as Likely benign.
Frequency
Consequence
NM_021228.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAF1 | NM_021228.3 | c.847G>T | p.Asp283Tyr | missense_variant | 7/11 | ENST00000360565.8 | |
SCAF1 | XM_011527194.4 | c.856G>T | p.Asp286Tyr | missense_variant | 7/11 | ||
SCAF1 | XM_005259122.6 | c.847G>T | p.Asp283Tyr | missense_variant | 7/11 | ||
SCAF1 | XM_017027083.3 | c.577G>T | p.Asp193Tyr | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAF1 | ENST00000360565.8 | c.847G>T | p.Asp283Tyr | missense_variant | 7/11 | 2 | NM_021228.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 27
GnomAD4 exome Cov.: 37
GnomAD4 genome Cov.: 27
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2022 | The c.847G>T (p.D283Y) alteration is located in exon 7 (coding exon 6) of the SCAF1 gene. This alteration results from a G to T substitution at nucleotide position 847, causing the aspartic acid (D) at amino acid position 283 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
Publications
No publications associated with this variant yet.