Variant chr13-32443085-A-AT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

The NM_001320836.3(N4BP2L2):c.2738_2739insA(p.Asn913LysfsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,454,142 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

N4BP2L2
NM_001320836.3 frameshift

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 0.123

Variant links:

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]

N4BP2L2 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 13-32443085-A-AT is Pathogenic according to our data. Variant chr13-32443085-A-AT is described in ClinVar as [Pathogenic]. Clinvar id is 599575.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
N4BP2L2	NM_001278432.2 linkuse as main transcript	c.1406_1407insA	p.Asn469LysfsTer2	frameshift_variant	7/10	NP_001265361.1
N4BP2L2	NM_001320836.3 linkuse as main transcript	c.2738_2739insA	p.Asn913LysfsTer2	frameshift_variant	7/10	NP_001307765.1
N4BP2L2	NM_001387001.1 linkuse as main transcript	c.2738_2739insA	p.Asn913LysfsTer2	frameshift_variant	7/10	NP_001373930.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
N4BP2L2	ENST00000380121.7 linkuse as main transcript	n.1422_1423insA		non_coding_transcript_exon_variant	5/8	1
N4BP2L2	ENST00000357505.10 linkuse as main transcript	c.1406_1407insA	p.Asn469LysfsTer2	frameshift_variant	7/10	2	ENSP00000350104
N4BP2L2	ENST00000399396.7 linkuse as main transcript	c.1451_1452insA	p.Asn484LysfsTer2	frameshift_variant	7/10	5	ENSP00000382328	Q92802-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000206

AC:

AN:

1454142

Hom.:

Cov.:

AF XY:

0.00000415

AC XY:

AN XY:

722944

show subpopulations

Gnomad4 AFR exome

AF:

0.0000305

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Short stature

Pathogenic:1

Pathogenic, no assertion criteria provided

case-control

Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg

Nov 18, 2001

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over