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. Variant has been reported in ClinVar as (no stars).

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030571.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDFIP1	NM_030571.4	MANE Select	c.152-117A>G		intron	N/A	NP_085048.1	Q9BT67-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NDFIP1	ENST00000253814.6	TSL:1 MANE Select	c.152-117A>G	intron	N/A	ENSP00000253814.3	Q9BT67-1
NDFIP1	ENST00000856982.1		c.227-117A>G	intron	N/A	ENSP00000527041.1
NDFIP1	ENST00000944183.1		c.152-117A>G	intron	N/A	ENSP00000614242.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over