Genetic Variant NDFIP1:c.152-117A>G (chr5-142132095-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 NM_030571.4(NDFIP1):c.152-117A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,246,824 control chromosomes in the GnomAD database, including 9,289 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 0.11 ( 1226 hom., cov: 33)

Exomes 𝑓: 0.10 ( 8063 hom. )

Consequence

NDFIP1
NM_030571.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368

Publications

4 publications found

Variant links:

Genes affected

NDFIP1 (HGNC:17592): (Nedd4 family interacting protein 1) The protein encoded by this gene belongs to a small group of evolutionarily conserved proteins with three transmembrane domains. It is a potential target for ubiquitination by the Nedd4 family of proteins. This protein is thought to be part of a family of integral Golgi membrane proteins. [provided by RefSeq, Jul 2008]

NDFIP1 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDFIP1	NM_030571.4 link	c.152-117A>G		intron_variant	Intron 2 of 7	ENST00000253814.6	NP_085048.1	Q9BT67-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDFIP1	ENST00000253814.6 link	c.152-117A>G		intron_variant	Intron 2 of 7	1	NM_030571.4	ENSP00000253814.3		Q9BT67-1
NDFIP1	ENST00000509436.1 link	n.538A>G		non_coding_transcript_exon_variant	Exon 2 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16346

AN:

152124

Hom.:

1225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0772

Gnomad AMI

AF:

0.0450

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.0755

Gnomad EAS

AF:

0.367

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.0909

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0843

Gnomad OTH

AF:

0.111

GnomAD4 exome

AF:

0.104

AC:

114125

AN:

1094582

Hom.:

8063

Cov.:

AF XY:

0.106

AC XY:

57458

AN XY:

544552

show subpopulations

African (AFR)

AF:

0.0758

AC:

1876

AN:

24742

American (AMR)

AF:

0.273

AC:

5545

AN:

20276

Ashkenazi Jewish (ASJ)

AF:

0.0732

AC:

1311

AN:

17912

East Asian (EAS)

AF:

0.366

AC:

13083

AN:

35708

South Asian (SAS)

AF:

0.145

AC:

8554

AN:

59152

European-Finnish (FIN)

AF:

0.101

AC:

4835

AN:

47680

Middle Eastern (MID)

AF:

0.0934

AC:

437

AN:

4678

European-Non Finnish (NFE)

AF:

0.0874

AC:

73239

AN:

837666

Other (OTH)

AF:

0.112

AC:

5245

AN:

46768

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

4902

9804

14706

19608

24510

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2798

5596

8394

11192

13990

<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:

0.108

AC:

16375

AN:

152242

Hom.:

1226

Cov.:

AF XY:

0.111

AC XY:

8279

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0772

AC:

3207

AN:

41552

American (AMR)

AF:

0.214

AC:

3269

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0755

AC:

262

AN:

3472

East Asian (EAS)

AF:

0.366

AC:

1899

AN:

5184

South Asian (SAS)

AF:

0.149

AC:

720

AN:

4830

European-Finnish (FIN)

AF:

0.0909

AC:

964

AN:

10606

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0844

AC:

5736

AN:

68002

Other (OTH)

AF:

0.114

AC:

241

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

717

1435

2152

2870

3587

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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:

0.108

Hom.:

381

Bravo

AF:

0.120

Asia WGS

AF:

0.215

AC:

750

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.040

(source)

DANN

Benign

0.68

PhyloP100

-0.37

Mutation Taster

=100/0

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