22-43540326-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022785.4(EFCAB6):āc.3680A>Gā(p.Asn1227Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,614,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022785.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFCAB6 | NM_022785.4 | c.3680A>G | p.Asn1227Ser | missense_variant | 28/32 | ENST00000262726.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFCAB6 | ENST00000262726.12 | c.3680A>G | p.Asn1227Ser | missense_variant | 28/32 | 2 | NM_022785.4 | P1 | |
EFCAB6 | ENST00000396231.6 | c.3224A>G | p.Asn1075Ser | missense_variant | 26/30 | 1 | |||
EFCAB6 | ENST00000461800.5 | n.317A>G | non_coding_transcript_exon_variant | 3/7 | 1 | ||||
EFCAB6-AS1 | ENST00000656483.1 | n.249-18291T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251452Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135916
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727236
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 17, 2023 | The c.3680A>G (p.N1227S) alteration is located in exon 28 (coding exon 26) of the EFCAB6 gene. This alteration results from a A to G substitution at nucleotide position 3680, causing the asparagine (N) at amino acid position 1227 to be replaced by a serine (S). 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