rs11614925

chr12-76067266-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004537.7(NAP1L1):c.206+105T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 828,100 control chromosomes in the GnomAD database, including 15,025 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 (2260 hom., cov: 31)
  • Exomes 𝑓: 0.18 (12765 hom.)
• Consequence: NAP1L1 NM_004537.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

NAP1L1 (HGNC:7637): (nucleosome assembly protein 1 like 1) This gene encodes a member of the nucleosome assembly protein (NAP) family. This protein participates in DNA replication and may play a role in modulating chromatin formation and contribute to the regulation of cell proliferation. Alternative splicing results in multiple transcript variants encoding different isoforms; however, not all have been fully described. [provided by RefSeq, Apr 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAP1L1	NM_004537.7	c.206+105T>C		intron_variant		ENST00000618691.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAP1L1	ENST00000618691.5	c.206+105T>C		intron_variant		1	NM_004537.7	P1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25213 AN: 151972 Hom.: 2259 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.203

GnomAD4 exome AF: 0.184 AC: 124142 AN: 676008 Hom.: 12765 AF XY: 0.191 AC XY: 66910 AN XY: 351050

Gnomad4 AFR exome AF: 0.123

Gnomad4 AMR exome AF: 0.143

Gnomad4 ASJ exome AF: 0.233

Gnomad4 EAS exome AF: 0.0281

Gnomad4 SAS exome AF: 0.314

Gnomad4 FIN exome AF: 0.152

Gnomad4 NFE exome AF: 0.185

Gnomad4 OTH exome AF: 0.190

GnomAD4 genome AF: 0.166 AC: 25222 AN: 152092 Hom.: 2260 Cov.: 31 AF XY: 0.166 AC XY: 12371 AN XY: 74376

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.0362

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.202

Alfa AF: 0.191 Hom.: 2843

Bravo AF: 0.163

Asia WGS AF: 0.168 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	8.9
Dann	Benign	0.43

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

LitVar

Other links and lift over

dbSNP: rs11614925; hg19: chr12-76461046;