rs369694920
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182542.3(ERICH6B):c.1993G>A(p.Ala665Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000354 in 1,551,800 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A665V) has been classified as Likely benign.
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.1993G>A | p.Ala665Thr | missense_variant | Exon 15 of 15 | ENST00000298738.3 | NP_872348.2 | |
ERICH6B | XM_011534965.3 | c.2065G>A | p.Ala689Thr | missense_variant | Exon 14 of 14 | XP_011533267.1 | ||
ERICH6B | XM_017020418.2 | c.1993G>A | p.Ala665Thr | missense_variant | Exon 14 of 14 | XP_016875907.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152042Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000888 AC: 14AN: 157742Hom.: 0 AF XY: 0.0000959 AC XY: 8AN XY: 83406
GnomAD4 exome AF: 0.0000336 AC: 47AN: 1399758Hom.: 0 Cov.: 30 AF XY: 0.0000420 AC XY: 29AN XY: 690382
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1993G>A (p.A665T) 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 1993, causing the alanine (A) at amino acid position 665 to be replaced by a threonine (T). 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