chr22-37373956-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_052906.5(ELFN2):c.1579G>T(p.Gly527Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000026 in 1,460,752 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G527S) has been classified as Uncertain significance.
Frequency
Consequence
NM_052906.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELFN2 | NM_052906.5 | c.1579G>T | p.Gly527Cys | missense_variant | 3/3 | ENST00000402918.7 | |
ELFN2 | NR_110512.2 | n.183-31253G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELFN2 | ENST00000402918.7 | c.1579G>T | p.Gly527Cys | missense_variant | 3/3 | 4 | NM_052906.5 | P1 | |
ELFN2 | ENST00000452946.1 | n.149-31253G>T | intron_variant, non_coding_transcript_variant | 4 | |||||
ELFN2 | ENST00000430883.5 | n.434+10894G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250810Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135744
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1460752Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 726712
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 07, 2022 | The c.1579G>T (p.G527C) alteration is located in exon 3 (coding exon 1) of the ELFN2 gene. This alteration results from a G to T substitution at nucleotide position 1579, causing the glycine (G) at amino acid position 527 to be replaced by a cysteine (C). 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