rs17147990

Variant names:

• chr4-70033205-T-A
• rs17147990
• NM_000200.3:c.141T>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000200.3(HTN3):​c.141T>A​(p.Tyr47*) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 5 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0441 AC: 6705 AN: 152054 Hom.: 500 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0161

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.0321

GnomAD2 exomes AF: 0.0104 AC: 2569 AN: 246454 AF XY: 0.00724

Gnomad AFR exome AF: 0.149

Gnomad AMR exome AF: 0.00552

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000186

Gnomad OTH exome AF: 0.00318

GnomAD4 exome AF: 0.00399 AC: 5775 AN: 1447332 Hom.: 398 Cov.: 28 AF XY: 0.00334 AC XY: 2404 AN XY: 720424

African (AFR) AF: 0.148 AC: 4776 AN: 32362

American (AMR) AF: 0.00698 AC: 306 AN: 43850

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26024

East Asian (EAS) AF: 0.00 AC: 0 AN: 39364

South Asian (SAS) AF: 0.000260 AC: 22 AN: 84504

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53260

Middle Eastern (MID) AF: 0.00489 AC: 28 AN: 5726

European-Non Finnish (NFE) AF: 0.0000680 AC: 75 AN: 1102358

Other (OTH) AF: 0.00949 AC: 568 AN: 59884

GnomAD4 genome AF: 0.0442 AC: 6719 AN: 152172 Hom.: 503 Cov.: 32 AF XY: 0.0426 AC XY: 3170 AN XY: 74406

African (AFR) AF: 0.154 AC: 6385 AN: 41512

American (AMR) AF: 0.0160 AC: 245 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00103 AC: 5 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.000235 AC: 16 AN: 67962

Other (OTH) AF: 0.0318 AC: 67 AN: 2110

Alfa AF: 0.00666 Hom.: 55

Bravo AF: 0.0500

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.145 AC: 641

ESP6500EA AF: 0.000465 AC: 4

ExAC AF: 0.0137 AC: 1667

Asia WGS AF: 0.0100 AC: 35 AN: 3478

EpiCase AF: 0.000110

EpiControl AF: 0.000179

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.40	T
BayesDel_noAF	Benign	-0.20
CADD	Pathogenic	35
DANN	Benign	0.89
Eigen	Benign	-0.33
Eigen_PC	Benign	-0.81
FATHMM_MKL	Benign	0.0045	N
PhyloP100		0.32
Vest4		0.43
GERP RS		-2.8
Mutation Taster		=189/11	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17147990; hg19: chr4-70898922;