14-74494108-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_194279.4(ISCA2):āc.130G>Cā(p.Glu44Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000666 in 1,576,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_194279.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISCA2 | NM_194279.4 | c.130G>C | p.Glu44Gln | missense_variant | 2/4 | ENST00000556816.6 | |
ISCA2 | NM_001272007.2 | c.130G>C | p.Glu44Gln | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISCA2 | ENST00000556816.6 | c.130G>C | p.Glu44Gln | missense_variant | 2/4 | 1 | NM_194279.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000363 AC: 69AN: 189828Hom.: 0 AF XY: 0.000348 AC XY: 36AN XY: 103552
GnomAD4 exome AF: 0.0000597 AC: 85AN: 1423748Hom.: 0 Cov.: 31 AF XY: 0.0000609 AC XY: 43AN XY: 705606
GnomAD4 genome AF: 0.000131 AC: 20AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at