NM_024867.4:c.1262G>A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_024867.4(SPEF2):c.1262G>A(p.Arg421His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0116 in 1,612,356 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_024867.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPEF2 | NM_024867.4 | c.1262G>A | p.Arg421His | missense_variant | Exon 9 of 37 | ENST00000356031.8 | NP_079143.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00725 AC: 1103AN: 152180Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00768 AC: 1917AN: 249766Hom.: 11 AF XY: 0.00838 AC XY: 1131AN XY: 134902
GnomAD4 exome AF: 0.0121 AC: 17631AN: 1460058Hom.: 137 Cov.: 31 AF XY: 0.0122 AC XY: 8847AN XY: 726176
GnomAD4 genome AF: 0.00724 AC: 1102AN: 152298Hom.: 2 Cov.: 33 AF XY: 0.00694 AC XY: 517AN XY: 74476
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
- -
SPEF2: BP4, BS1, BS2 -
not specified Uncertain:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Candidate PCD gene, but frequency is high -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at