Genetic Variant NDFIP1:c.563-1136C>T (chr5-142143435-C-T) – 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.563-1136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,996 control chromosomes in the GnomAD database, including 34,665 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 0.67 ( 34632 hom., cov: 30)

Exomes 𝑓: 0.60 ( 33 hom. )

Consequence

NDFIP1
NM_030571.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Publications

38 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:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDFIP1	NM_030571.4 link	c.563-1136C>T		intron_variant	Intron 6 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.563-1136C>T		intron_variant	Intron 6 of 7	1	NM_030571.4	ENSP00000253814.3		Q9BT67-1
NDFIP1	ENST00000503388.1 link	n.458C>T		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.672

AC:

101987

AN:

151690

Hom.:

34593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.769

Gnomad AMI

AF:

0.635

Gnomad AMR

AF:

0.680

Gnomad ASJ

AF:

0.703

Gnomad EAS

AF:

0.645

Gnomad SAS

AF:

0.562

Gnomad FIN

AF:

0.661

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.622

Gnomad OTH

AF:

0.678

GnomAD4 exome

AF:

0.597

AC:

111

AN:

186

Hom.:

Cov.:

AF XY:

0.618

AC XY:

AN XY:

110

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.545

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.667

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.602

AC:

AN:

128

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.672

AC:

102072

AN:

151810

Hom.:

34632

Cov.:

AF XY:

0.671

AC XY:

49807

AN XY:

74176

show subpopulations

African (AFR)

AF:

0.768

AC:

31778

AN:

41354

American (AMR)

AF:

0.680

AC:

10376

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.703

AC:

2439

AN:

3468

East Asian (EAS)

AF:

0.645

AC:

3309

AN:

5132

South Asian (SAS)

AF:

0.562

AC:

2697

AN:

4796

European-Finnish (FIN)

AF:

0.661

AC:

6965

AN:

10530

Middle Eastern (MID)

AF:

0.707

AC:

208

AN:

294

European-Non Finnish (NFE)

AF:

0.622

AC:

42303

AN:

67964

Other (OTH)

AF:

0.675

AC:

1420

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1639

3279

4918

6558

8197

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.644

Hom.:

76407

Bravo

AF:

0.681

Asia WGS

AF:

0.609

AC:

2123

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

9.5

(source)

DANN

Benign

0.72

PhyloP100

1.0

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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5-142143435-C-T

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