22-37373355-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_052906.5(ELFN2):c.2180G>A(p.Arg727His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,024 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ELFN2 | ENST00000402918.7 | c.2180G>A | p.Arg727His | missense_variant | Exon 3 of 3 | 4 | NM_052906.5 | ENSP00000385277.1 | ||
ELFN2 | ENST00000430883.5 | n.434+11495G>A | intron_variant | Intron 1 of 2 | 2 | |||||
ELFN2 | ENST00000452946.1 | n.149-30652G>A | intron_variant | Intron 1 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248988Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135106
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460858Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 726708
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2180G>A (p.R727H) 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 2180, causing the arginine (R) at amino acid position 727 to be replaced by a histidine (H). 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