chr5-142132095-A-T

Variant names:

• chr5-142132095-A-T
• rs10515512
• NM_030571.4:c.152-117A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_030571.4(NDFIP1):​c.152-117A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000913 in 1,095,476 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 9.1e-7 (0 hom.)
• Consequence: NDFIP1 NM_030571.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030571.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDFIP1	NM_030571.4	MANE Select	c.152-117A>T		intron	N/A	NP_085048.1	Q9BT67-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDFIP1	ENST00000253814.6	TSL:1 MANE Select	c.152-117A>T		intron	N/A	ENSP00000253814.3	Q9BT67-1
	NDFIP1	ENST00000856982.1		c.227-117A>T		intron	N/A	ENSP00000527041.1
	NDFIP1	ENST00000944183.1		c.152-117A>T		intron	N/A	ENSP00000614242.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 9.13e-7 AC: 1 AN: 1095476 Hom.: 0 Cov.: 14 AF XY: 0.00000183 AC XY: 1 AN XY: 544984

African (AFR) AF: 0.00 AC: 0 AN: 24752

American (AMR) AF: 0.00 AC: 0 AN: 20308

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17918

East Asian (EAS) AF: 0.00 AC: 0 AN: 35758

South Asian (SAS) AF: 0.00 AC: 0 AN: 59204

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47690

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4680

European-Non Finnish (NFE) AF: 0.00000119 AC: 1 AN: 838356

Other (OTH) AF: 0.00 AC: 0 AN: 46810

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.018
DANN	Benign	0.67
PhyloP100		-0.37

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

Other links and lift over

dbSNP: rs10515512; hg19: chr5-141511660;