rs72658840
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001277115.2(DNAH11):c.13547C>T(p.Ala4516Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00536 in 1,601,468 control chromosomes in the GnomAD database, including 310 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001277115.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH11 | NM_001277115.2 | c.13547C>T | p.Ala4516Val | missense_variant | 82/82 | ENST00000409508.8 | NP_001264044.1 | |
CDCA7L | NM_018719.5 | c.*1072G>A | 3_prime_UTR_variant | 10/10 | ENST00000406877.8 | NP_061189.2 | ||
CDCA7L | NM_001127370.3 | c.*1072G>A | 3_prime_UTR_variant | 11/11 | NP_001120842.1 | |||
CDCA7L | NM_001127371.3 | c.*1072G>A | 3_prime_UTR_variant | 9/9 | NP_001120843.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH11 | ENST00000409508.8 | c.13547C>T | p.Ala4516Val | missense_variant | 82/82 | 5 | NM_001277115.2 | ENSP00000475939 | P1 | |
CDCA7L | ENST00000406877.8 | c.*1072G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_018719.5 | ENSP00000383986 | P1 | ||
CDCA7L | ENST00000356195.9 | c.*1072G>A | 3_prime_UTR_variant | 11/11 | 2 | ENSP00000348523 | ||||
CDCA7L | ENST00000488845.1 | n.1594G>A | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0262 AC: 3847AN: 146778Hom.: 169 Cov.: 32
GnomAD3 exomes AF: 0.00685 AC: 1641AN: 239448Hom.: 64 AF XY: 0.00522 AC XY: 677AN XY: 129758
GnomAD4 exome AF: 0.00325 AC: 4724AN: 1454598Hom.: 140 Cov.: 33 AF XY: 0.00282 AC XY: 2040AN XY: 722758
GnomAD4 genome AF: 0.0262 AC: 3855AN: 146870Hom.: 170 Cov.: 32 AF XY: 0.0247 AC XY: 1775AN XY: 71742
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2013 | Ala4516Val in exon 82 of DNAH11: This variant is not expected to have clinical s ignificance because it has been identified in 7.6% (301/3954) of African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs72658840). - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Primary ciliary dyskinesia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 17, 2021 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Primary ciliary dyskinesia 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at