rs57809907
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PVS1_ModerateBP6_Very_StrongBA1
The NM_130810.4(DNAAF4):c.1249G>T(p.Glu417*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,611,952 control chromosomes in the GnomAD database, including 13,397 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_130810.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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DNAAF4 | NM_130810.4 | c.1249G>T | p.Glu417* | stop_gained | Exon 10 of 10 | ENST00000321149.7 | NP_570722.2 | |
DNAAF4 | NM_001033559.3 | c.*12G>T | 3_prime_UTR_variant | Exon 9 of 9 | NP_001028731.1 | |||
DNAAF4 | NM_001033560.2 | c.1047+4221G>T | intron_variant | Intron 8 of 8 | NP_001028732.1 | |||
DNAAF4-CCPG1 | NR_037923.1 | n.1408+1813G>T | intron_variant | Intron 8 of 15 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.178 AC: 27025AN: 151988Hom.: 4172 Cov.: 32
GnomAD3 exomes AF: 0.104 AC: 26061AN: 250812Hom.: 2430 AF XY: 0.102 AC XY: 13830AN XY: 135566
GnomAD4 exome AF: 0.0964 AC: 140755AN: 1459846Hom.: 9219 Cov.: 31 AF XY: 0.0965 AC XY: 70106AN XY: 726294
GnomAD4 genome AF: 0.178 AC: 27065AN: 152106Hom.: 4178 Cov.: 32 AF XY: 0.175 AC XY: 13000AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:3
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This variant is associated with the following publications: (PMID: 23341075, 12954984, 31213628) -
not specified Benign:2
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: Frequency, variant associated with dyslexia -
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Primary ciliary dyskinesia 25 Benign:1
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Dyslexia, susceptibility to, 1 Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at