6-154833252-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014892.5(SCAF8):c.3673C>T(p.Pro1225Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014892.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCAF8 | ENST00000367178.8 | c.3673C>T | p.Pro1225Ser | missense_variant | 20/20 | 2 | NM_014892.5 | ENSP00000356146.3 | ||
SCAF8 | ENST00000417268.3 | c.3907C>T | p.Pro1303Ser | missense_variant | 21/21 | 2 | ENSP00000413098.2 | |||
SCAF8 | ENST00000367186.7 | c.3871C>T | p.Pro1291Ser | missense_variant | 22/22 | 2 | ENSP00000356154.4 | |||
TIAM2 | ENST00000461783 | c.-718C>T | 5_prime_UTR_variant | 1/29 | 2 | ENSP00000437188.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461730Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727164
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.3673C>T (p.P1225S) alteration is located in exon 20 (coding exon 20) of the SCAF8 gene. This alteration results from a C to T substitution at nucleotide position 3673, causing the proline (P) at amino acid position 1225 to be replaced by a serine (S). 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