4-140543512-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_153702.4(ELMOD2):c.662G>A(p.Ser221Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000913 in 1,606,730 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S221T) has been classified as Uncertain significance.
Frequency
Consequence
NM_153702.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELMOD2 | NM_153702.4 | c.662G>A | p.Ser221Asn | missense_variant | 8/9 | ENST00000323570.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELMOD2 | ENST00000323570.8 | c.662G>A | p.Ser221Asn | missense_variant | 8/9 | 1 | NM_153702.4 | P1 | |
ELMOD2 | ENST00000502290.1 | n.278G>A | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
ELMOD2 | ENST00000512057.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000750 AC: 114AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000993 AC: 243AN: 244610Hom.: 1 AF XY: 0.00109 AC XY: 145AN XY: 132548
GnomAD4 exome AF: 0.000930 AC: 1353AN: 1454532Hom.: 2 Cov.: 30 AF XY: 0.000965 AC XY: 698AN XY: 723664
GnomAD4 genome ? AF: 0.000749 AC: 114AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.000712 AC XY: 53AN XY: 74418
ClinVar
Submissions by phenotype
ELMOD2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 02, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at