7-741343-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017802.4(DNAAF5):c.906-4T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 1,585,028 control chromosomes in the GnomAD database, including 525,722 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_017802.4 splice_region, intron
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 |
---|---|---|---|---|---|---|---|---|
DNAAF5 | NM_017802.4 | c.906-4T>G | splice_region_variant, intron_variant | Intron 3 of 12 | ENST00000297440.11 | NP_060272.3 | ||
DNAAF5 | XM_024446813.2 | c.906-4T>G | splice_region_variant, intron_variant | Intron 3 of 11 | XP_024302581.1 | |||
DNAAF5 | NR_075098.2 | n.866-4T>G | splice_region_variant, intron_variant | Intron 3 of 12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAAF5 | ENST00000297440.11 | c.906-4T>G | splice_region_variant, intron_variant | Intron 3 of 12 | 1 | NM_017802.4 | ENSP00000297440.6 | |||
DNAAF5 | ENST00000440747.5 | c.309-4T>G | splice_region_variant, intron_variant | Intron 3 of 12 | 2 | ENSP00000403165.1 | ||||
DNAAF5 | ENST00000437419.5 | c.222-4T>G | splice_region_variant, intron_variant | Intron 2 of 4 | 5 | ENSP00000410788.1 | ||||
DNAAF5 | ENST00000438961.1 | n.375-4T>G | splice_region_variant, intron_variant | Intron 3 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.782 AC: 118999AN: 152116Hom.: 46863 Cov.: 35
GnomAD3 exomes AF: 0.802 AC: 168499AN: 210076Hom.: 67982 AF XY: 0.811 AC XY: 91385AN XY: 112660
GnomAD4 exome AF: 0.816 AC: 1169273AN: 1432796Hom.: 478822 Cov.: 32 AF XY: 0.818 AC XY: 580841AN XY: 710182
GnomAD4 genome AF: 0.782 AC: 119092AN: 152232Hom.: 46900 Cov.: 35 AF XY: 0.780 AC XY: 58057AN XY: 74430
ClinVar
Submissions by phenotype
not specified Benign:2
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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 -
Primary ciliary dyskinesia Benign:2
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This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Primary ciliary dyskinesia 18 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at