rs17147990
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_000200.3(HTN3):c.141T>A(p.Tyr47Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00781 in 1,599,504 control chromosomes in the GnomAD database, including 901 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as no classification for the single variant (no stars).
Frequency
Genomes: 𝑓 0.044 ( 503 hom., cov: 32)
Exomes 𝑓: 0.0040 ( 398 hom. )
Consequence
HTN3
NM_000200.3 stop_gained
NM_000200.3 stop_gained
Scores
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.318
Genes affected
HTN3 (HGNC:5284): (histatin 3) This gene encodes a member of the histatin family of small, histidine-rich, cationic proteins. They function as antimicrobial peptides and are important components of the innate immune system. Histatins are found in saliva and exhibit antibacterial, antifungal activities and function in wound healing. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTN3 | NM_000200.3 | c.141T>A | p.Tyr47Ter | stop_gained | 5/6 | ENST00000673563.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTN3 | ENST00000673563.1 | c.141T>A | p.Tyr47Ter | stop_gained | 5/6 | NM_000200.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0441 AC: 6705AN: 152054Hom.: 500 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0104 AC: 2569AN: 246454Hom.: 167 AF XY: 0.00724 AC XY: 965AN XY: 133294
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GnomAD4 exome AF: 0.00399 AC: 5775AN: 1447332Hom.: 398 Cov.: 28 AF XY: 0.00334 AC XY: 2404AN XY: 720424
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GnomAD4 genome ? AF: 0.0442 AC: 6719AN: 152172Hom.: 503 Cov.: 32 AF XY: 0.0426 AC XY: 3170AN XY: 74406
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ESP6500AA
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
P;P;P
Vest4
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at