rs7226310
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_199242.3(UNC13D):c.754-31C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 1,610,762 control chromosomes in the GnomAD database, including 3,960 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.096 ( 1238 hom., cov: 32)
Exomes 𝑓: 0.049 ( 2722 hom. )
Consequence
UNC13D
NM_199242.3 intron
NM_199242.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.41
Genes affected
UNC13D (HGNC:23147): (unc-13 homolog D) This gene encodes a protein that is a member of the UNC13 family, containing similar domain structure as other family members but lacking an N-terminal phorbol ester-binding C1 domain present in other Munc13 proteins. The protein appears to play a role in vesicle maturation during exocytosis and is involved in regulation of cytolytic granules secretion. Mutations in this gene are associated with familial hemophagocytic lymphohistiocytosis type 3, a genetically heterogeneous, rare autosomal recessive disorder. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 17-75840360-G-A is Benign according to our data. Variant chr17-75840360-G-A is described in ClinVar as [Benign]. Clinvar id is 263244.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC13D | NM_199242.3 | c.754-31C>T | intron_variant | ENST00000207549.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC13D | ENST00000207549.9 | c.754-31C>T | intron_variant | 1 | NM_199242.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0957 AC: 14549AN: 152020Hom.: 1232 Cov.: 32
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GnomAD3 exomes AF: 0.0579 AC: 14312AN: 246982Hom.: 748 AF XY: 0.0580 AC XY: 7773AN XY: 134098
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GnomAD4 exome AF: 0.0495 AC: 72199AN: 1458626Hom.: 2722 Cov.: 34 AF XY: 0.0505 AC XY: 36663AN XY: 725652
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GnomAD4 genome ? AF: 0.0958 AC: 14575AN: 152136Hom.: 1238 Cov.: 32 AF XY: 0.0948 AC XY: 7052AN XY: 74388
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at