rs207650

Variant names:

• chr13-32487100-A-G
• rs207650
• NM_001320836.3:c.1697+30757T>C

Variant summary

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

The NM_001320836.3(N4BP2L2):​c.1697+30757T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,010 control chromosomes in the GnomAD database, including 11,372 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 0.38 (11372 hom., cov: 32)
• Consequence: N4BP2L2 NM_001320836.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 8 publications found

Genes affected

N4BP2L2 (HGNC:26916): (NEDD4 binding protein 2 like 2) Enables enzyme binding activity. Involved in negative regulation of hematopoietic stem cell differentiation and positive regulation of hematopoietic stem cell proliferation. Located in nucleus. Part of transcription repressor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
N4BP2L2	NM_001320836.3	c.1697+30757T>C		intron_variant	Intron 6 of 9		NP_001307765.1
N4BP2L2	NM_001387001.1	c.1697+30757T>C		intron_variant	Intron 6 of 9		NP_001373930.1
N4BP2L2	NM_001387002.1	c.1697+30757T>C		intron_variant	Intron 6 of 9		NP_001373931.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
N4BP2L2	ENST00000674422.1	c.1697+30757T>C		intron_variant	Intron 7 of 7			ENSP00000501390.1
N4BP2L2	ENST00000399396.7	c.410+30757T>C		intron_variant	Intron 6 of 9	5		ENSP00000382328.3
N4BP2L2	ENST00000357505.10	c.365+30757T>C		intron_variant	Intron 6 of 9	2		ENSP00000350104.6

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58404 AN: 151890 Hom.: 11363 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.385 AC: 58451 AN: 152010 Hom.: 11372 Cov.: 32 AF XY: 0.382 AC XY: 28410 AN XY: 74302

African (AFR) AF: 0.412 AC: 17067 AN: 41452

American (AMR) AF: 0.298 AC: 4546 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3470

East Asian (EAS) AF: 0.467 AC: 2404 AN: 5148

South Asian (SAS) AF: 0.388 AC: 1871 AN: 4824

European-Finnish (FIN) AF: 0.375 AC: 3972 AN: 10584

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25980 AN: 67948

Other (OTH) AF: 0.366 AC: 774 AN: 2114

Alfa AF: 0.385 Hom.: 1476

Bravo AF: 0.379

Asia WGS AF: 0.391 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs207650; hg19: chr13-33061237;