5-142143435-C-T

Position:

• chr5-142143435-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.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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
NDFIP1	NM_030571.4	c.563-1136C>T		intron_variant		ENST00000253814.6	NP_085048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDFIP1	ENST00000253814.6	c.563-1136C>T		intron_variant		1	NM_030571.4	ENSP00000253814.3
NDFIP1	ENST00000503388.1	n.458C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.672 AC: 101987 AN: 151690 Hom.: 34593 Cov.: 30

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.: 33 Cov.: 0 AF XY: 0.618 AC XY: 68 AN XY: 110

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.545

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.602

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.672 AC: 102072 AN: 151810 Hom.: 34632 Cov.: 30 AF XY: 0.671 AC XY: 49807 AN XY: 74176

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.675

Alfa AF: 0.630 Hom.: 50034

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
DANN	Benign	0.72

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: rs1062158; hg19: chr5-141523000;