7-56116300-T-G

Variant names:

• chr7-56116300-T-G
• NM_001145712.2:c.15A>C

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001145712.2(NUPR2):​c.15A>C​(p.Ala5Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,169,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A5A) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.00010 (0 hom.)
• Consequence: NUPR2 NM_001145712.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

NUPR2 (HGNC:44164): (nuclear protein 2, transcriptional regulator) Involved in several processes, including cellular response to starvation; negative regulation of cell population proliferation; and negative regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP7: Synonymous conserved (PhyloP=-2.16 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUPR2	NM_001145712.2	c.15A>C	p.Ala5Ala	synonymous_variant	Exon 1 of 2	ENST00000329309.4	NP_001139184.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUPR2	ENST00000329309.4	c.15A>C	p.Ala5Ala	synonymous_variant	Exon 1 of 2	1	NM_001145712.2	ENSP00000455442.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.000100 AC: 117 AN: 1169038 Hom.: 0 Cov.: 30 AF XY: 0.0000916 AC XY: 53 AN XY: 578292

Gnomad4 AFR exome AF: 0.0000478

Gnomad4 AMR exome AF: 0.000496

Gnomad4 ASJ exome AF: 0.000230

Gnomad4 EAS exome AF: 0.000492

Gnomad4 SAS exome AF: 0.0000153

Gnomad4 FIN exome AF: 0.000617

Gnomad4 NFE exome AF: 0.0000629

Gnomad4 OTH exome AF: 0.000172

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
DANN	Benign	0.37

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-56183993;