5-142108799-G-C

Position:

• chr5-142108799-G-C

Variant summary

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

The NM_030571.4(NDFIP1):​c.-176G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 443,966 control chromosomes in the GnomAD database, including 27,686 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 0.28 (7503 hom., cov: 32)
  • Exomes 𝑓: 0.37 (20183 hom.)
• Consequence: NDFIP1 NM_030571.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDFIP1	NM_030571.4	c.-176G>C		5_prime_UTR_variant	1/8	ENST00000253814.6	NP_085048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDFIP1	ENST00000253814	c.-176G>C		5_prime_UTR_variant	1/8	1	NM_030571.4	ENSP00000253814.3
NDFIP1	ENST00000509436.1	n.12G>C		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42443 AN: 151470 Hom.: 7505 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.369 AC: 107848 AN: 292386 Hom.: 20183 Cov.: 5 AF XY: 0.370 AC XY: 55674 AN XY: 150566

Gnomad4 AFR exome AF: 0.0826

Gnomad4 AMR exome AF: 0.304

Gnomad4 ASJ exome AF: 0.405

Gnomad4 EAS exome AF: 0.208

Gnomad4 SAS exome AF: 0.276

Gnomad4 FIN exome AF: 0.412

Gnomad4 NFE exome AF: 0.399

Gnomad4 OTH exome AF: 0.348

GnomAD4 genome AF: 0.280 AC: 42436 AN: 151580 Hom.: 7503 Cov.: 32 AF XY: 0.279 AC XY: 20692 AN XY: 74072

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.305

Alfa AF: 0.208 Hom.: 530

Bravo AF: 0.263

Asia WGS AF: 0.233 AC: 805 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	15
DANN	Benign	0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.0

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: rs3761759; hg19: chr5-141488364;