rs3752447

Variant names:

• chr13-32407005-C-T
• rs3752447
• NM_052818.3:c.396+245G>A

Variant summary

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

The NM_052818.3(N4BP2L1):​c.396+245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 513,526 control chromosomes in the GnomAD database, including 10,282 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 0.17 (2525 hom., cov: 32)
  • Exomes 𝑓: 0.19 (7757 hom.)
• Consequence: N4BP2L1 NM_052818.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462

Genes affected

N4BP2L1 (HGNC:25037): (NEDD4 binding protein 2 like 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
N4BP2L1	NM_052818.3	c.396+245G>A		intron_variant	Intron 3 of 4	ENST00000380130.7	NP_438169.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
N4BP2L1	ENST00000380130.7	c.396+245G>A		intron_variant	Intron 3 of 4	1	NM_052818.3	ENSP00000369473.2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26495 AN: 152034 Hom.: 2526 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.189

GnomAD4 exome AF: 0.192 AC: 69406 AN: 361374 Hom.: 7757 Cov.: 3 AF XY: 0.192 AC XY: 36980 AN XY: 192590

Gnomad4 AFR exome AF: 0.140

Gnomad4 AMR exome AF: 0.173

Gnomad4 ASJ exome AF: 0.196

Gnomad4 EAS exome AF: 0.439

Gnomad4 SAS exome AF: 0.165

Gnomad4 FIN exome AF: 0.109

Gnomad4 NFE exome AF: 0.183

Gnomad4 OTH exome AF: 0.188

GnomAD4 genome AF: 0.174 AC: 26510 AN: 152152 Hom.: 2525 Cov.: 32 AF XY: 0.172 AC XY: 12826 AN XY: 74404

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.0978

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.190

Alfa AF: 0.186 Hom.: 3189

Bravo AF: 0.181

Asia WGS AF: 0.253 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.76

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: rs3752447; hg19: chr13-32981142;