Genetic Variant NM_000200.3:c.141T>A (chr4-70033205-T-A) – ACMG Classification: Benign (-8 pts)

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.318

Publications

5 publications found

Variant links:

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]

HTN3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTN3	NM_000200.3 link	c.141T>A	p.Tyr47*	stop_gained	Exon 5 of 6	ENST00000673563.1	NP_000191.1	P15516

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTN3	ENST00000673563.1 link	c.141T>A	p.Tyr47*	stop_gained	Exon 5 of 6		NM_000200.3	ENSP00000500623.1		P15516

Frequencies

GnomAD3 genomes

AF:

0.0441

AC:

6705

AN:

152054

Hom.:

500

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.00334

AC XY:

2404

AN XY:

720424

show subpopulations

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:

AN:

26024

East Asian (EAS)

AF:

0.00

AC:

AN:

39364

South Asian (SAS)

AF:

0.000260

AC:

AN:

84504

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53260

Middle Eastern (MID)

AF:

0.00489

AC:

AN:

5726

European-Non Finnish (NFE)

AF:

0.0000680

AC:

AN:

1102358

Other (OTH)

AF:

0.00949

AC:

568

AN:

59884

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.427

Heterozygous variant carriers

205

410

614

819

1024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

138

276

414

552

690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0442

AC:

6719

AN:

152172

Hom.:

503

Cov.:

AF XY:

0.0426

AC XY:

3170

AN XY:

74406

show subpopulations

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:

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

5172

South Asian (SAS)

AF:

0.00103

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.00342

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000235

AC:

AN:

67962

Other (OTH)

AF:

0.0318

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

292

583

875

1166

1458

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00666

Hom.:

Bravo

AF:

0.0500

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.145

AC:

641

ESP6500EA

AF:

0.000465

AC:

ExAC

AF:

0.0137

AC:

1667

Asia WGS

AF:

0.0100

AC:

AN:

3478

EpiCase

AF:

0.000110

EpiControl

AF:

0.000179

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.20

CADD

Pathogenic

(source)

DANN

Benign

0.89

Eigen

Benign

-0.33

Eigen_PC

Benign

-0.81

FATHMM_MKL

Benign

0.0045

PhyloP100

0.32

Vest4

0.43

GERP RS

-2.8

Mutation Taster

=189/11

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over