chr13-45541656-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182542.3(ERICH6B):c.1897G>A(p.Glu633Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000903 in 1,550,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182542.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ERICH6B | NM_182542.3 | c.1897G>A | p.Glu633Lys | missense_variant | Exon 15 of 15 | ENST00000298738.3 | NP_872348.2 | |
ERICH6B | XM_011534965.3 | c.1969G>A | p.Glu657Lys | missense_variant | Exon 14 of 14 | XP_011533267.1 | ||
ERICH6B | XM_017020418.2 | c.1897G>A | p.Glu633Lys | missense_variant | Exon 14 of 14 | XP_016875907.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000134 AC: 21AN: 156628Hom.: 0 AF XY: 0.000108 AC XY: 9AN XY: 83004
GnomAD4 exome AF: 0.0000651 AC: 91AN: 1398392Hom.: 0 Cov.: 34 AF XY: 0.0000638 AC XY: 44AN XY: 689702
GnomAD4 genome AF: 0.000322 AC: 49AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1897G>A (p.E633K) alteration is located in exon 15 (coding exon 13) of the ERICH6B gene. This alteration results from a G to A substitution at nucleotide position 1897, causing the glutamic acid (E) at amino acid position 633 to be replaced by a lysine (K). 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