11-73951088-T-A
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_153614.4(DNAJB13):c.19T>A(p.Ser7Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000535 in 1,614,086 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S7S) has been classified as Likely benign.
Frequency
Consequence
NM_153614.4 missense
Scores
Clinical Significance
Conservation
Publications
- primary ciliary dyskinesia 34Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae)
- primary ciliary dyskinesiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152208Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00108 AC: 271AN: 250360 AF XY: 0.00141 show subpopulations
GnomAD4 exome AF: 0.000558 AC: 815AN: 1461760Hom.: 7 Cov.: 30 AF XY: 0.000778 AC XY: 566AN XY: 727176 show subpopulations
GnomAD4 genome AF: 0.000315 AC: 48AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74492 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:3
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DNAJB13: BP4, BS2 -
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DNAJB13-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at