NM_031427.4:c.532+11C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_031427.4(DNAL1):c.532+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 1,586,552 control chromosomes in the GnomAD database, including 3,111 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_031427.4 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 |
---|---|---|---|---|---|---|---|---|
DNAL1 | NM_031427.4 | c.532+11C>T | intron_variant | Intron 7 of 7 | ENST00000553645.7 | NP_113615.2 | ||
DNAL1 | NM_001201366.2 | c.415+11C>T | intron_variant | Intron 8 of 8 | NP_001188295.1 | |||
DNAL1 | XM_017021679.3 | c.415+11C>T | intron_variant | Intron 8 of 8 | XP_016877168.1 | |||
DNAL1 | XM_024449715.2 | c.415+11C>T | intron_variant | Intron 8 of 8 | XP_024305483.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0461 AC: 7013AN: 152042Hom.: 202 Cov.: 31
GnomAD3 exomes AF: 0.0496 AC: 10282AN: 207444Hom.: 288 AF XY: 0.0501 AC XY: 5553AN XY: 110738
GnomAD4 exome AF: 0.0615 AC: 88178AN: 1434392Hom.: 2909 Cov.: 32 AF XY: 0.0608 AC XY: 43164AN XY: 710424
GnomAD4 genome AF: 0.0461 AC: 7008AN: 152160Hom.: 202 Cov.: 31 AF XY: 0.0443 AC XY: 3297AN XY: 74400
ClinVar
Submissions by phenotype
not specified Benign:2
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415+11C>T in intron 8 of DNAL1: This variant is not expected to have clinical si gnificance because it is not located within the conserved splice consensus seque nce. It has been identified in 6.5% (537/8256) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.was hington.edu/EVS; dbSNP rs72721725). -
not provided Benign:2
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Primary ciliary dyskinesia 16 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at