chr19-49061735-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_006179.5(NTF4):c.263C>T(p.Ala88Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00334 in 1,611,310 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0025 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0034 ( 38 hom. )

Consequence

NTF4
NM_006179.5 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts U:1B:2

Conservation

PhyloP100: 1.65

Variant links:

Genes affected

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 links:

ENSG00000283663 (HGNC:):

ENSG00000283663 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 19-49061735-G-A is Benign according to our data. Variant chr19-49061735-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 14017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00253 (386/152332) while in subpopulation SAS AF = 0.0189 (91/4824). AF 95% confidence interval is 0.0157. There are 3 homozygotes in GnomAd4. There are 196 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.

BS2

High AC in GnomAd4 at 386 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTF4	NM_006179.5 link	c.263C>T	p.Ala88Val	missense_variant	Exon 2 of 2	ENST00000593537.2	NP_006170.1	P34130A0A024QZE4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTF4	ENST00000593537.2 link	c.263C>T	p.Ala88Val	missense_variant	Exon 2 of 2	6	NM_006179.5	ENSP00000469455.1		P34130
ENSG00000283663	ENST00000599795.5 link	n.243+20C>T		intron_variant	Intron 3 of 6	2		ENSP00000470689.1		M0QZQ0

Frequencies

GnomAD3 genomes

AF:

0.00255

AC:

388

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000362

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.00183

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0191

Gnomad FIN

AF:

0.000847

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00295

Gnomad OTH

AF:

0.00382

GnomAD2 exomes

AF:

0.00454

AC:

1093

AN:

240822

AF XY:

0.00536

show subpopulations

Gnomad AFR exome

AF:

0.000476

Gnomad AMR exome

AF:

0.00186

Gnomad ASJ exome

AF:

0.00631

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000532

Gnomad NFE exome

AF:

0.00349

Gnomad OTH exome

AF:

0.00556

GnomAD4 exome

AF:

0.00343

AC:

4998

AN:

1458978

Hom.:

Cov.:

AF XY:

0.00391

AC XY:

2836

AN XY:

725736

show subpopulations

Gnomad4 AFR exome

AF:

0.000509

AC:

AN:

33392

Gnomad4 AMR exome

AF:

0.00169

AC:

AN:

44460

Gnomad4 ASJ exome

AF:

0.00633

AC:

165

AN:

26076

Gnomad4 EAS exome

AF:

0.0000253

AC:

AN:

39580

Gnomad4 SAS exome

AF:

0.0178

AC:

1532

AN:

86004

Gnomad4 FIN exome

AF:

0.000459

AC:

AN:

52324

Gnomad4 NFE exome

AF:

0.00256

AC:

2846

AN:

1111122

Gnomad4 Remaining exome

AF:

0.00405

AC:

244

AN:

60256

Heterozygous variant carriers

340

680

1021

1361

1701

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

116

232

348

464

580

<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:

0.00253

AC:

386

AN:

152332

Hom.:

Cov.:

AF XY:

0.00263

AC XY:

196

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.000361

AC:

0.00036082

AN:

0.00036082

Gnomad4 AMR

AF:

0.00183

AC:

0.00182935

AN:

0.00182935

Gnomad4 ASJ

AF:

0.00548

AC:

0.00547866

AN:

0.00547866

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.0189

AC:

0.018864

AN:

0.018864

Gnomad4 FIN

AF:

0.000847

AC:

0.000847298

AN:

0.000847298

Gnomad4 NFE

AF:

0.00295

AC:

0.00295449

AN:

0.00295449

Gnomad4 OTH

AF:

0.00378

AC:

0.0037843

AN:

0.0037843

Heterozygous variant carriers

108

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<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:

0.00325

Hom.:

Bravo

AF:

0.00234

TwinsUK

AF:

0.00216

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.000460

AC:

ESP6500EA

AF:

0.00317

AC:

ExAC

AF:

0.00469

AC:

567

Asia WGS

AF:

0.00693

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Uncertain:1Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Glaucoma 1, open angle, O

Uncertain:1

Mar 12, 2010

OMIM

Significance:Uncertain significance

Review Status:no assertion criteria provided

Collection Method:literature only

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Intellectual disability, X-linked 99

Benign:1

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:research

The heterozygous p.Ala88Val variant in NTF4 has been identified in at least 13 individuals with glaucoma and at least 19 individuals without glaucoma (PMID: 19765683, 20215012, 20463313), but has also been identified in >2% of South Asian chromosomes and 8 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely benign for autosomal dominant primary open angle glaucoma. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.13

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.22

T;.

Eigen

Benign

-0.20

Eigen_PC

Benign

-0.22

FATHMM_MKL

Benign

0.22

LIST_S2

Benign

0.64

T;T

MetaRNN

Benign

0.022

T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-0.69

N;.

PrimateAI

Uncertain

0.55

Sift4G

Benign

0.48

T;.

Polyphen

1.0

D;.

Vest4

0.32

MVP

0.78

ClinPred

0.030

GERP RS

3.5

Varity_R

0.11

gMVP

0.24

Mutation Taster

=99/1

polymorphism

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.22

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.22

Position offset: 2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over