rs9545133

Variant names:

• chr13-79547847-T-C
• rs9545133
• NM_019080.3:c.841-481T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The NM_019080.3(NDFIP2):​c.841-481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 152,222 control chromosomes in the GnomAD database, including 45 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 0.019 (45 hom., cov: 32)
• Consequence: NDFIP2 NM_019080.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08

Genes affected

NDFIP2 (HGNC:18537): (Nedd4 family interacting protein 2) Enables WW domain binding activity. Involved in negative regulation of gene expression; negative regulation of transport; and positive regulation of protein ubiquitination. Located in several cellular components, including Golgi apparatus; mitochondrion; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0188 (2869/152222) while in subpopulation NFE AF= 0.0294 (1996/67964). AF 95% confidence interval is 0.0283. There are 45 homozygotes in gnomad4. There are 1375 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 45 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDFIP2	NM_019080.3	c.841-481T>C		intron_variant	Intron 5 of 7	ENST00000218652.12	NP_061953.2
NDFIP2	NM_001394685.1	c.838-481T>C		intron_variant	Intron 5 of 7		NP_001381614.1
NDFIP2	NM_001161407.2	c.781-481T>C		intron_variant	Intron 5 of 7		NP_001154879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDFIP2	ENST00000218652.12	c.841-481T>C		intron_variant	Intron 5 of 7	1	NM_019080.3	ENSP00000218652.7

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 2868 AN: 152104 Hom.: 45 Cov.: 32

Gnomad AFR AF: 0.00529

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00538

Gnomad FIN AF: 0.0203

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0211

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0188 AC: 2869 AN: 152222 Hom.: 45 Cov.: 32 AF XY: 0.0185 AC XY: 1375 AN XY: 74426

Gnomad4 AFR AF: 0.00527

Gnomad4 AMR AF: 0.0171

Gnomad4 ASJ AF: 0.0161

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00559

Gnomad4 FIN AF: 0.0203

Gnomad4 NFE AF: 0.0294

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0232 Hom.: 4

Bravo AF: 0.0177

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	17
DANN	Benign	0.84

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: rs9545133; hg19: chr13-80121982;