chr20-10038537-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022096.6(ANKEF1):c.236G>A(p.Arg79Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022096.6 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 |
---|---|---|---|---|---|---|---|---|
ANKEF1 | NM_022096.6 | c.236G>A | p.Arg79Gln | missense_variant | 3/11 | ENST00000378392.6 | NP_071379.3 | |
SNAP25-AS1 | NR_040710.1 | n.500-11889C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKEF1 | ENST00000378392.6 | c.236G>A | p.Arg79Gln | missense_variant | 3/11 | 1 | NM_022096.6 | ENSP00000367644 | P1 | |
SNAP25-AS1 | ENST00000421143.6 | n.235-11889C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251422Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135876
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461886Hom.: 0 Cov.: 33 AF XY: 0.0000633 AC XY: 46AN XY: 727242
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.236G>A (p.R79Q) alteration is located in exon 3 (coding exon 1) of the ANKEF1 gene. This alteration results from a G to A substitution at nucleotide position 236, causing the arginine (R) at amino acid position 79 to be replaced by a glutamine (Q). 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