6-154832100-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014892.5(SCAF8):āc.2521A>Gā(p.Ile841Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,613,984 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 (ā ).
Frequency
Consequence
NM_014892.5 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 |
---|---|---|---|---|---|---|---|
SCAF8 | NM_014892.5 | c.2521A>G | p.Ile841Val | missense_variant | 20/20 | ENST00000367178.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAF8 | ENST00000367178.8 | c.2521A>G | p.Ile841Val | missense_variant | 20/20 | 2 | NM_014892.5 | P1 | |
SCAF8 | ENST00000417268.3 | c.2755A>G | p.Ile919Val | missense_variant | 21/21 | 2 | |||
SCAF8 | ENST00000367186.7 | c.2719A>G | p.Ile907Val | missense_variant | 22/22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000995 AC: 25AN: 251176Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135756
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461816Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727210
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.2521A>G (p.I841V) alteration is located in exon 20 (coding exon 20) of the SCAF8 gene. This alteration results from a A to G substitution at nucleotide position 2521, causing the isoleucine (I) at amino acid position 841 to be replaced by a valine (V). 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