5-35641489-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024867.4(SPEF2):c.220G>A(p.Gly74Ser) variant causes a missense change. The variant allele was found at a frequency of 0.05 in 1,613,610 control chromosomes in the GnomAD database, including 2,246 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_024867.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPEF2 | NM_024867.4 | c.220G>A | p.Gly74Ser | missense_variant | Exon 3 of 37 | ENST00000356031.8 | NP_079143.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0538 AC: 8182AN: 151966Hom.: 253 Cov.: 32
GnomAD3 exomes AF: 0.0513 AC: 12881AN: 251194Hom.: 358 AF XY: 0.0487 AC XY: 6614AN XY: 135764
GnomAD4 exome AF: 0.0496 AC: 72460AN: 1461526Hom.: 1993 Cov.: 33 AF XY: 0.0486 AC XY: 35345AN XY: 727076
GnomAD4 genome AF: 0.0539 AC: 8190AN: 152084Hom.: 253 Cov.: 32 AF XY: 0.0544 AC XY: 4044AN XY: 74328
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at