chr13-32412082-A-G

Variant names:

• chr13-32412082-A-G
• rs206319
• NM_052818.3:c.180-4310T>C

Variant summary

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

The NM_052818.3(N4BP2L1):​c.180-4310T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,466 control chromosomes in the GnomAD database, including 7,373 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 0.31 (7373 hom., cov: 30)
• Consequence: N4BP2L1 NM_052818.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	N4BP2L1	NM_052818.3	MANE Select	c.180-4310T>C		intron	N/A	NP_438169.2	Q5TBK1-1
	N4BP2L1	NM_001353627.2		c.455+3877T>C		intron	N/A	NP_001340556.1
	N4BP2L1	NM_001353628.2		c.455+3877T>C		intron	N/A	NP_001340557.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	N4BP2L1	ENST00000380130.7	TSL:1 MANE Select	c.180-4310T>C		intron	N/A	ENSP00000369473.2	Q5TBK1-1
	N4BP2L1	ENST00000380133.6	TSL:1	c.180-4310T>C		intron	N/A	ENSP00000369476.2	Q5TBK1-1
	N4BP2L1	ENST00000380139.8	TSL:1	c.180-4310T>C		intron	N/A	ENSP00000369484.3	Q5TBK1-2

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46733 AN: 151350 Hom.: 7369 Cov.: 30

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.309 AC: 46755 AN: 151466 Hom.: 7373 Cov.: 30 AF XY: 0.310 AC XY: 22909 AN XY: 73972

African (AFR) AF: 0.261 AC: 10747 AN: 41250

American (AMR) AF: 0.289 AC: 4405 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 934 AN: 3462

East Asian (EAS) AF: 0.316 AC: 1622 AN: 5130

South Asian (SAS) AF: 0.390 AC: 1877 AN: 4812

European-Finnish (FIN) AF: 0.328 AC: 3438 AN: 10470

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22708 AN: 67800

Other (OTH) AF: 0.309 AC: 650 AN: 2104

Alfa AF: 0.326 Hom.: 31034

Bravo AF: 0.304

Asia WGS AF: 0.318 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.71
PhyloP100		0.22
PromoterAI		-0.0016	Neutral
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: rs206319; hg19: chr13-32986219;