HTN3 p.Tyr47*

Variant names:

• chr4-70033205-T-G
• NM_000200.3:c.141T>G
• HTN3 p.Tyr47*

Your query was ambiguous. Multiple possible variants found:

• chr4-70033205-T-G
• chr4-70033205-T-A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_000200.3(HTN3):​c.141T>G​(p.Tyr47*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HTN3 NM_000200.3 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000200.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTN3	NM_000200.3	MANE Select	c.141T>G	p.Tyr47*	stop_gained	Exon 5 of 6	NP_000191.1	P15516

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTN3	ENST00000673563.1	MANE Select	c.141T>G	p.Tyr47*	stop_gained	Exon 5 of 6	ENSP00000500623.1	P15516
	HTN3	ENST00000530128.5	TSL:2	c.141T>G	p.Tyr47*	stop_gained	Exon 5 of 6	ENSP00000432561.1	P15516
	HTN3	ENST00000381057.3	TSL:2	c.111T>G	p.Tyr37*	stop_gained	Exon 4 of 5	ENSP00000370445.3	X6RAH8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.042	T
BayesDel_noAF	Benign	-0.18
CADD	Pathogenic	35
DANN	Benign	0.90
Eigen	Benign	-0.33
Eigen_PC	Benign	-0.81
FATHMM_MKL	Benign	0.015	N
PhyloP100		0.32
Mutation Taster		=189/11	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr4-70898922;