14-49634073-G-C
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_018139.3(DNAAF2):c.1077C>G(p.Val359Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000391 in 1,534,310 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_018139.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAAF2 | NM_018139.3 | c.1077C>G | p.Val359Val | synonymous_variant | Exon 1 of 3 | ENST00000298292.13 | NP_060609.2 | |
DNAAF2 | NM_001083908.2 | c.1077C>G | p.Val359Val | synonymous_variant | Exon 1 of 2 | NP_001077377.1 | ||
DNAAF2 | NM_001378453.1 | c.-795C>G | upstream_gene_variant | NP_001365382.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAAF2 | ENST00000298292.13 | c.1077C>G | p.Val359Val | synonymous_variant | Exon 1 of 3 | 1 | NM_018139.3 | ENSP00000298292.8 | ||
DNAAF2 | ENST00000406043.3 | c.1077C>G | p.Val359Val | synonymous_variant | Exon 1 of 2 | 1 | ENSP00000384862.3 |
Frequencies
GnomAD3 genomes AF: 0.000881 AC: 134AN: 152124Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00107 AC: 139AN: 129360Hom.: 1 AF XY: 0.000963 AC XY: 68AN XY: 70606
GnomAD4 exome AF: 0.000337 AC: 466AN: 1382078Hom.: 5 Cov.: 88 AF XY: 0.000341 AC XY: 232AN XY: 681320
GnomAD4 genome AF: 0.000880 AC: 134AN: 152232Hom.: 1 Cov.: 33 AF XY: 0.00136 AC XY: 101AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:1
p.Val359Val in exon 1 of DNAAF2: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 1.1% (172/15154) of Finnish chromosomes including 1 homozygote by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs765764624). ACMG/AMP Criteri a applied: BA1, BP4, BP7. -
Primary ciliary dyskinesia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at