chr15-60448884-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024611.6(ICE2):c.2083T>G(p.Ser695Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,600,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 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
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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 |
---|---|---|---|---|---|---|---|
ICE2 | NM_024611.6 | c.2083T>G | p.Ser695Ala | missense_variant | 10/16 | ENST00000261520.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ICE2 | ENST00000261520.9 | c.2083T>G | p.Ser695Ala | missense_variant | 10/16 | 1 | NM_024611.6 | P1 | |
ICE2 | ENST00000561328.1 | n.1139T>G | non_coding_transcript_exon_variant | 2/3 | 1 | ||||
ICE2 | ENST00000558181.5 | c.*1701T>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/16 | 1 | ||||
ICE2 | ENST00000561144.1 | n.68T>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000843 AC: 2AN: 237216Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 128436
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1447926Hom.: 0 Cov.: 32 AF XY: 0.00000278 AC XY: 2AN XY: 719710
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.2083T>G (p.S695A) alteration is located in exon 10 (coding exon 9) of the ICE2 gene. This alteration results from a T to G substitution at nucleotide position 2083, causing the serine (S) at amino acid position 695 to be replaced by an alanine (A). 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