chr8-131944763-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_015137.6(EFR3A):c.106G>A(p.Asp36Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000557 in 1,598,746 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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. D36H) has been classified as Uncertain significance.
Frequency
Consequence
NM_015137.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFR3A | NM_015137.6 | c.106G>A | p.Asp36Asn | missense_variant | 3/23 | ENST00000254624.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFR3A | ENST00000254624.10 | c.106G>A | p.Asp36Asn | missense_variant | 3/23 | 1 | NM_015137.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152034Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000387 AC: 9AN: 232312Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 124906
GnomAD4 exome AF: 0.0000518 AC: 75AN: 1446712Hom.: 1 Cov.: 30 AF XY: 0.0000376 AC XY: 27AN XY: 718582
GnomAD4 genome ? AF: 0.0000921 AC: 14AN: 152034Hom.: 1 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74242
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.106G>A (p.D36N) alteration is located in exon 3 (coding exon 3) of the EFR3A gene. This alteration results from a G to A substitution at nucleotide position 106, causing the aspartic acid (D) at amino acid position 36 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