chr13-32407005-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052818.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	N4BP2L1	NM_052818.3	MANE Select	c.396+245G>A		intron	N/A	NP_438169.2
	N4BP2L1	NM_001353627.2		c.672+245G>A		intron	N/A	NP_001340556.1
	N4BP2L1	NM_001353628.2		c.672+245G>A		intron	N/A	NP_001340557.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	N4BP2L1	ENST00000380130.7	TSL:1 MANE Select	c.396+245G>A		intron	N/A	ENSP00000369473.2
	N4BP2L1	ENST00000380133.6	TSL:1	c.396+245G>A		intron	N/A	ENSP00000369476.2
	N4BP2L1	ENST00000380139.8	TSL:1	c.396+245G>A		intron	N/A	ENSP00000369484.3

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

African (AFR) AF: 0.140 AC: 1474 AN: 10532

American (AMR) AF: 0.173 AC: 2618 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 2117 AN: 10778

East Asian (EAS) AF: 0.439 AC: 10163 AN: 23134

South Asian (SAS) AF: 0.165 AC: 6863 AN: 41538

European-Finnish (FIN) AF: 0.109 AC: 2214 AN: 20322

Middle Eastern (MID) AF: 0.193 AC: 300 AN: 1554

European-Non Finnish (NFE) AF: 0.183 AC: 39780 AN: 217776

Other (OTH) AF: 0.188 AC: 3877 AN: 20624

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

African (AFR) AF: 0.141 AC: 5834 AN: 41506

American (AMR) AF: 0.179 AC: 2737 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 678 AN: 3472

East Asian (EAS) AF: 0.404 AC: 2092 AN: 5172

South Asian (SAS) AF: 0.166 AC: 803 AN: 4828

European-Finnish (FIN) AF: 0.0978 AC: 1035 AN: 10588

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12553 AN: 67986

Other (OTH) AF: 0.190 AC: 401 AN: 2114

Alfa AF: 0.186 Hom.: 4421

Bravo AF: 0.181

Asia WGS AF: 0.253 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.46
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: rs3752447; hg19: chr13-32981142;