5-142152170-C-T

Position:

• chr5-142152170-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
NDFIP1	NM_030571.4	c.*442C>T		3_prime_UTR_variant	8/8	ENST00000253814.6	NP_085048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDFIP1	ENST00000253814.6	c.*442C>T		3_prime_UTR_variant	8/8	1	NM_030571.4	ENSP00000253814	P1
NDFIP1	ENST00000503388.1	n.2139C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142527 AN: 152162 Hom.: 66819 Cov.: 32

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.: 0 AF XY: 0.932 AC XY: 313 AN XY: 336

Gnomad4 EAS exome AF: 0.913

Gnomad4 FIN exome AF: 0.946

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.937 AC: 142645 AN: 152280 Hom.: 66877 Cov.: 32 AF XY: 0.940 AC XY: 69957 AN XY: 74458

Gnomad4 AFR AF: 0.947

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.981

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.938

Alfa AF: 0.925 Hom.: 64070

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	14
DANN	Benign	0.48

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

LitVar

Other links and lift over

dbSNP: rs249637; hg19: chr5-141531735;