5-173232683-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004387.4(NKX2-5):c.861C>A(p.Ala287Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,458,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A287A) has been classified as Benign.
Frequency
Consequence
NM_004387.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NKX2-5 | NM_004387.4 | c.861C>A | p.Ala287Ala | synonymous_variant | Exon 2 of 2 | ENST00000329198.5 | NP_004378.1 | |
NKX2-5 | NM_001166176.2 | c.*660C>A | 3_prime_UTR_variant | Exon 2 of 2 | NP_001159648.1 | |||
NKX2-5 | NM_001166175.2 | c.*814C>A | 3_prime_UTR_variant | Exon 2 of 2 | NP_001159647.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247808Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134948
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458774Hom.: 0 Cov.: 34 AF XY: 0.00000276 AC XY: 2AN XY: 725200
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Atrial septal defect 7 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at