3-113291589-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PVS1_ModerateBP6_ModerateBS1BS2
The NM_001164496.2(CFAP44):c.5533C>T(p.Arg1845*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000417 in 1,537,194 control chromosomes in the GnomAD database, including 13 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00032 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00043 ( 12 hom. )
Consequence
CFAP44
NM_001164496.2 stop_gained
NM_001164496.2 stop_gained
Scores
1
2
4
Clinical Significance
Conservation
PhyloP100: 1.76
Genes affected
CFAP44 (HGNC:25631): (cilia and flagella associated protein 44) Enables peptidase activity. Involved in sperm axoneme assembly. Acts upstream of or within microtubule cytoskeleton organization. Predicted to be located in cytoplasm; cytoskeleton; and motile cilium. Implicated in spermatogenic failure 20. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.00575 CDS is truncated, and there are 1 pathogenic variants in the truncated region.
BP6
Variant 3-113291589-G-A is Benign according to our data. Variant chr3-113291589-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 724581.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000315 (48/152254) while in subpopulation SAS AF= 0.00872 (42/4818). AF 95% confidence interval is 0.00663. There are 1 homozygotes in gnomad4. There are 41 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 12 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152136Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000893 AC: 129AN: 144416Hom.: 2 AF XY: 0.00122 AC XY: 94AN XY: 77104
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GnomAD4 exome AF: 0.000428 AC: 593AN: 1384940Hom.: 12 Cov.: 30 AF XY: 0.000632 AC XY: 432AN XY: 683392
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GnomAD4 genome AF: 0.000315 AC: 48AN: 152254Hom.: 1 Cov.: 33 AF XY: 0.000551 AC XY: 41AN XY: 74432
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Benign
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
N
Vest4
ClinPred
T
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at