Genetic Variant NDFIP1:c.*442C>T (chr5-142152170-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.*442C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.937 in 152,850 control chromosomes in the GnomAD database, including 67,127 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 0.94 ( 66877 hom., cov: 32)

Exomes 𝑓: 0.94 ( 250 hom. )

Consequence

NDFIP1
NM_030571.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.58

Publications

7 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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDFIP1	NM_030571.4 link	c.*442C>T		3_prime_UTR_variant	Exon 8 of 8	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.*442C>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_030571.4	ENSP00000253814.3		Q9BT67-1
NDFIP1	ENST00000503388.1 link	n.2139C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.937

AC:

142527

AN:

152162

Hom.:

66819

Cov.:

show subpopulations

Gnomad AFR

AF:

0.947

Gnomad AMI

AF:

0.944

Gnomad AMR

AF:

0.944

Gnomad ASJ

AF:

0.877

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.981

Gnomad FIN

AF:

0.951

Gnomad MID

AF:

0.899

Gnomad NFE

AF:

0.922

Gnomad OTH

AF:

0.937

GnomAD4 exome

AF:

0.939

AC:

535

AN:

570

Hom.:

250

Cov.:

AF XY:

0.932

AC XY:

313

AN XY:

336

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.913

AC:

126

AN:

138

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.946

AC:

403

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

GnomAD4 genome

AF:

0.937

AC:

142645

AN:

152280

Hom.:

66877

Cov.:

AF XY:

0.940

AC XY:

69957

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.947

AC:

39329

AN:

41552

American (AMR)

AF:

0.945

AC:

14444

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.877

AC:

3039

AN:

3466

East Asian (EAS)

AF:

0.999

AC:

5183

AN:

5188

South Asian (SAS)

AF:

0.981

AC:

4739

AN:

4830

European-Finnish (FIN)

AF:

0.951

AC:

10089

AN:

10608

Middle Eastern (MID)

AF:

0.905

AC:

266

AN:

294

European-Non Finnish (NFE)

AF:

0.922

AC:

62713

AN:

68024

Other (OTH)

AF:

0.938

AC:

1982

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

451

903

1354

1806

2257

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

910

1820

2730

3640

4550

<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:

0.926

Hom.:

82468

Bravo

AF:

0.935

Asia WGS

AF:

0.988

AC:

3434

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.48

PhyloP100

1.6

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