rs16976354
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_130810.4(DNAAF4):c.114C>A(p.Asn38Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 1,613,942 control chromosomes in the GnomAD database, including 1,552 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_130810.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF4 | NM_130810.4 | c.114C>A | p.Asn38Lys | missense_variant | 2/10 | ENST00000321149.7 | |
DNAAF4-CCPG1 | NR_037923.1 | n.369C>A | non_coding_transcript_exon_variant | 1/16 | |||
DNAAF4 | NM_001033560.2 | c.114C>A | p.Asn38Lys | missense_variant | 2/9 | ||
DNAAF4 | NM_001033559.3 | c.114C>A | p.Asn38Lys | missense_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF4 | ENST00000321149.7 | c.114C>A | p.Asn38Lys | missense_variant | 2/10 | 1 | NM_130810.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0548 AC: 8345AN: 152198Hom.: 784 Cov.: 32
GnomAD3 exomes AF: 0.0139 AC: 3492AN: 250676Hom.: 321 AF XY: 0.0100 AC XY: 1357AN XY: 135602
GnomAD4 exome AF: 0.00548 AC: 8008AN: 1461626Hom.: 766 Cov.: 32 AF XY: 0.00465 AC XY: 3379AN XY: 727112
GnomAD4 genome ? AF: 0.0549 AC: 8358AN: 152316Hom.: 786 Cov.: 32 AF XY: 0.0532 AC XY: 3961AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 26, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at