15-60448952-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024611.6(ICE2):c.2015A>G(p.Glu672Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,996 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024611.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ICE2 | NM_024611.6 | c.2015A>G | p.Glu672Gly | missense_variant | 10/16 | ENST00000261520.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ICE2 | ENST00000261520.9 | c.2015A>G | p.Glu672Gly | missense_variant | 10/16 | 1 | NM_024611.6 | P1 | |
ICE2 | ENST00000561328.1 | n.1071A>G | non_coding_transcript_exon_variant | 2/3 | 1 | ||||
ICE2 | ENST00000558181.5 | c.*1633A>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/16 | 1 | ||||
ICE2 | ENST00000561144.1 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250772Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135744
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461750Hom.: 1 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727172
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2023 | The c.2015A>G (p.E672G) alteration is located in exon 10 (coding exon 9) of the ICE2 gene. This alteration results from a A to G substitution at nucleotide position 2015, causing the glutamic acid (E) at amino acid position 672 to be replaced by a glycine (G). 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