rs10515512

chr5-142132095-A-G

Variant summary

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

The NM_030571.4(NDFIP1):c.152-117A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,246,824 control chromosomes in the GnomAD database, including 9,289 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 0.11 (1226 hom., cov: 33)
  • Exomes 𝑓: 0.10 (8063 hom.)
• Consequence: NDFIP1 NM_030571.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDFIP1	NM_030571.4	c.152-117A>G		intron_variant		ENST00000253814.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDFIP1	ENST00000253814.6	c.152-117A>G		intron_variant		1	NM_030571.4	P1
NDFIP1	ENST00000509436.1	n.538A>G		non_coding_transcript_exon_variant	2/3	5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16346 AN: 152124 Hom.: 1225 Cov.: 33

Gnomad AFR AF: 0.0772

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0909

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.104 AC: 114125 AN: 1094582 Hom.: 8063 Cov.: 14 AF XY: 0.106 AC XY: 57458 AN XY: 544552

Gnomad4 AFR exome AF: 0.0758

Gnomad4 AMR exome AF: 0.273

Gnomad4 ASJ exome AF: 0.0732

Gnomad4 EAS exome AF: 0.366

Gnomad4 SAS exome AF: 0.145

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.0874

Gnomad4 OTH exome AF: 0.112

GnomAD4 genome AF: 0.108 AC: 16375 AN: 152242 Hom.: 1226 Cov.: 33 AF XY: 0.111 AC XY: 8279 AN XY: 74442

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0909

Gnomad4 NFE AF: 0.0844

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0900 Hom.: 107

Bravo AF: 0.120

Asia WGS AF: 0.215 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.040
Dann	Benign	0.68

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: rs10515512; hg19: chr5-141511660; COSMIC: COSV54075710; COSMIC: COSV54075710;