2-53787239-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015701.5(ERLEC1):c.29G>A(p.Ser10Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 1,606,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_015701.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERLEC1 | NM_015701.5 | c.29G>A | p.Ser10Asn | missense_variant | 1/14 | ENST00000185150.9 | NP_056516.2 | |
ERLEC1 | NM_001127397.3 | c.29G>A | p.Ser10Asn | missense_variant | 1/13 | NP_001120869.1 | ||
ERLEC1 | NM_001127398.3 | c.29G>A | p.Ser10Asn | missense_variant | 1/13 | NP_001120870.1 | ||
GPR75-ASB3 | NM_001164165.2 | c.102-21654C>T | intron_variant | NP_001157637.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERLEC1 | ENST00000185150.9 | c.29G>A | p.Ser10Asn | missense_variant | 1/14 | 1 | NM_015701.5 | ENSP00000185150.4 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000288 AC: 7AN: 243258Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132212
GnomAD4 exome AF: 0.00000619 AC: 9AN: 1454022Hom.: 0 Cov.: 34 AF XY: 0.00000829 AC XY: 6AN XY: 723734
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 27, 2024 | The c.29G>A (p.S10N) alteration is located in exon 1 (coding exon 1) of the ERLEC1 gene. This alteration results from a G to A substitution at nucleotide position 29, causing the serine (S) at amino acid position 10 to be replaced by an asparagine (N). 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