chr4-140543512-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153702.4(ELMOD2):c.662G>C(p.Ser221Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000498 in 1,606,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S221N) has been classified as Likely benign.
Frequency
Consequence
NM_153702.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELMOD2 | NM_153702.4 | c.662G>C | p.Ser221Thr | missense_variant | 8/9 | ENST00000323570.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELMOD2 | ENST00000323570.8 | c.662G>C | p.Ser221Thr | missense_variant | 8/9 | 1 | NM_153702.4 | P1 | |
ELMOD2 | ENST00000502290.1 | n.278G>C | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
ELMOD2 | ENST00000512057.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000695 AC: 17AN: 244610Hom.: 0 AF XY: 0.0000604 AC XY: 8AN XY: 132548
GnomAD4 exome AF: 0.0000227 AC: 33AN: 1454540Hom.: 0 Cov.: 30 AF XY: 0.0000207 AC XY: 15AN XY: 723668
GnomAD4 genome ? AF: 0.000309 AC: 47AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2023 | The c.662G>C (p.S221T) alteration is located in exon 8 (coding exon 7) of the ELMOD2 gene. This alteration results from a G to C substitution at nucleotide position 662, causing the serine (S) at amino acid position 221 to be replaced by a threonine (T). 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