14-30734808-A-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_016106.4(SCFD1):c.1855A>C(p.Ile619Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,613,430 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_016106.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCFD1 | NM_016106.4 | c.1855A>C | p.Ile619Leu | missense_variant | 24/25 | ENST00000458591.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCFD1 | ENST00000458591.7 | c.1855A>C | p.Ile619Leu | missense_variant | 24/25 | 1 | NM_016106.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251140Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135726
GnomAD4 exome AF: 0.000179 AC: 261AN: 1461222Hom.: 0 Cov.: 29 AF XY: 0.000160 AC XY: 116AN XY: 726968
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2023 | The c.1855A>C (p.I619L) alteration is located in exon 24 (coding exon 24) of the SCFD1 gene. This alteration results from a A to C substitution at nucleotide position 1855, causing the isoleucine (I) at amino acid position 619 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