chr15-55836247-A-C

Variant names:

• chr15-55836247-A-C
• rs11630780
• NM_006154.4:c.2262+1542T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006154.4(NEDD4):​c.2262+1542T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,652 control chromosomes in the GnomAD database, including 12,485 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 0.40 (12485 hom., cov: 30)
• Consequence: NEDD4 NM_006154.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 6 publications found

Genes affected

NEDD4 (HGNC:7727): (NEDD4 E3 ubiquitin protein ligase) This gene is the founding member of the NEDD4 family of HECT ubiquitin ligases that function in the ubiquitin proteasome system of protein degradation. The encoded protein contains an N-terminal calcium and phospholipid binding C2 domain followed by multiple tryptophan-rich WW domains and, a C-terminal HECT ubiquitin ligase catalytic domain. It plays critical role in the regulation of a number of membrane receptors, endocytic machinery components and the tumor suppressor PTEN. [provided by RefSeq, Jul 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006154.4. 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
	NEDD4	NM_006154.4	MANE Select	c.2262+1542T>G		intron	N/A	NP_006145.2	P46934-4
	NEDD4	NM_001284338.2		c.3519+1542T>G		intron	N/A	NP_001271267.1	P46934-1
	NEDD4	NM_001284339.1		c.3471+1542T>G		intron	N/A	NP_001271268.1	P46934-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEDD4	ENST00000435532.8	TSL:1 MANE Select	c.2262+1542T>G		intron	N/A	ENSP00000410613.3	P46934-4
	NEDD4	ENST00000508342.5	TSL:1	c.3519+1542T>G		intron	N/A	ENSP00000424827.1	P46934-1
	NEDD4	ENST00000506154.1	TSL:1	c.3471+1542T>G		intron	N/A	ENSP00000422705.1	P46934-2

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60937 AN: 151534 Hom.: 12487 Cov.: 30

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.402 AC: 60960 AN: 151652 Hom.: 12485 Cov.: 30 AF XY: 0.402 AC XY: 29775 AN XY: 74070

African (AFR) AF: 0.373 AC: 15424 AN: 41310

American (AMR) AF: 0.406 AC: 6180 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1212 AN: 3464

East Asian (EAS) AF: 0.330 AC: 1695 AN: 5132

South Asian (SAS) AF: 0.481 AC: 2310 AN: 4806

European-Finnish (FIN) AF: 0.384 AC: 4028 AN: 10492

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28857 AN: 67928

Other (OTH) AF: 0.373 AC: 786 AN: 2108

Alfa AF: 0.367 Hom.: 2391

Bravo AF: 0.394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.26
DANN	Benign	0.49
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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: rs11630780; hg19: chr15-56128445;