dbSNP rs11669977: ENSG00000283663:n.243+888T>C (chr19-49060867-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000599795.5(ENSG00000283663):n.243+888T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 174,356 control chromosomes in the GnomAD database, including 2,592 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2286 hom., cov: 31)

Exomes 𝑓: 0.15 ( 306 hom. )

Consequence

ENSG00000283663
ENST00000599795.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.501

Publications

10 publications found

Variant links:

Genes affected

ENSG00000283663 (HGNC:):

ENSG00000283663 links:

NTF4 (HGNC:8024): (neurotrophin 4) This gene is a member of a family of neurotrophic factors, neurotrophins, that control survival and differentiation of mammalian neurons. The expression of this gene is ubiquitous and less influenced by environmental signals. While knock-outs of other neurotrophins including nerve growth factor, brain-derived neurotrophic factor, and neurotrophin 3 prove lethal during early postnatal development, NTF5-deficient mice only show minor cellular deficits and develop normally to adulthood. [provided by RefSeq, Jul 2008]

NTF4 Gene-Disease associations (from GenCC):

glaucoma 1, open angle, O
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

NTF4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTF4	XR_001753693.1 link	n.879+297T>C		intron_variant	Intron 2 of 2
NTF4	XR_001753694.1 link	n.880-58T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283663	ENST00000599795.5 link	n.243+888T>C		intron_variant	Intron 3 of 6	2		ENSP00000470689.1		M0QZQ0

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25579

AN:

151806

Hom.:

2285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.210

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.167

GnomAD4 exome

AF:

0.150

AC:

3354

AN:

22432

Hom.:

306

Cov.:

AF XY:

0.146

AC XY:

1683

AN XY:

11546

show subpopulations

African (AFR)

AF:

0.116

AC:

AN:

396

American (AMR)

AF:

0.221

AC:

600

AN:

2716

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

AN:

346

East Asian (EAS)

AF:

0.128

AC:

159

AN:

1244

South Asian (SAS)

AF:

0.103

AC:

269

AN:

2604

European-Finnish (FIN)

AF:

0.137

AC:

130

AN:

950

Middle Eastern (MID)

AF:

0.158

AC:

AN:

European-Non Finnish (NFE)

AF:

0.149

AC:

1948

AN:

13062

Other (OTH)

AF:

0.136

AC:

146

AN:

1076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

138

276

414

552

690

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

132

176

220

<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:

0.168

AC:

25591

AN:

151924

Hom.:

2286

Cov.:

AF XY:

0.166

AC XY:

12316

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.151

AC:

6272

AN:

41428

American (AMR)

AF:

0.210

AC:

3209

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

676

AN:

3464

East Asian (EAS)

AF:

0.160

AC:

824

AN:

5164

South Asian (SAS)

AF:

0.139

AC:

670

AN:

4808

European-Finnish (FIN)

AF:

0.128

AC:

1350

AN:

10572

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.176

AC:

11977

AN:

67930

Other (OTH)

AF:

0.170

AC:

356

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1074

2148

3222

4296

5370

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

276

552

828

1104

1380

<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:

0.178

Hom.:

3915

Bravo

AF:

0.177

Asia WGS

AF:

0.162

AC:

565

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.7

(source)

DANN

Benign

0.79

PhyloP100

0.50

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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