3-55992187-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015576.3(ERC2):c.2125G>A(p.Asp709Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015576.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ERC2 | ENST00000288221.11 | c.2125G>A | p.Asp709Asn | missense_variant | Exon 11 of 18 | 1 | NM_015576.3 | ENSP00000288221.6 | ||
ERC2 | ENST00000460849.5 | n.2125G>A | non_coding_transcript_exon_variant | Exon 11 of 19 | 1 | ENSP00000417445.1 | ||||
ERC2 | ENST00000492584.3 | c.2161G>A | p.Asp721Asn | missense_variant | Exon 12 of 18 | 5 | ENSP00000417280.3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000522 AC: 13AN: 249146Hom.: 0 AF XY: 0.0000666 AC XY: 9AN XY: 135148
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461590Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727088
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2125G>A (p.D709N) alteration is located in exon 11 (coding exon 10) of the ERC2 gene. This alteration results from a G to A substitution at nucleotide position 2125, causing the aspartic acid (D) at amino acid position 709 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