chr22-37374004-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052906.5(ELFN2):c.1531G>A(p.Gly511Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,613,094 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_052906.5 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 |
---|---|---|---|---|---|---|---|
ELFN2 | NM_052906.5 | c.1531G>A | p.Gly511Arg | missense_variant | 3/3 | ENST00000402918.7 | |
ELFN2 | NR_110512.2 | n.183-31301G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELFN2 | ENST00000402918.7 | c.1531G>A | p.Gly511Arg | missense_variant | 3/3 | 4 | NM_052906.5 | P1 | |
ELFN2 | ENST00000452946.1 | n.149-31301G>A | intron_variant, non_coding_transcript_variant | 4 | |||||
ELFN2 | ENST00000430883.5 | n.434+10846G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000919 AC: 23AN: 250258Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135504
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1460748Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 726704
GnomAD4 genome AF: 0.000190 AC: 29AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.1531G>A (p.G511R) alteration is located in exon 3 (coding exon 1) of the ELFN2 gene. This alteration results from a G to A substitution at nucleotide position 1531, causing the glycine (G) at amino acid position 511 to be replaced by an arginine (R). 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