11-2945063-C-G

Variant summary

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

The NM_005969.4(NAP1L4):c.*616G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,564 control chromosomes in the GnomAD database, including 6,391 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 0.25 (6387 hom., cov: 32)
  • Exomes 𝑓: 0.19 (4 hom.)
• Consequence: NAP1L4 NM_005969.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

Genes affected

NAP1L4 (HGNC:7640): (nucleosome assembly protein 1 like 4) This gene encodes a member of the nucleosome assembly protein (NAP) family which can interact with both core and linker histones. It can shuttle between the cytoplasm and nucleus, suggesting a role as a histone chaperone. This gene is one of several located near the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAP1L4	NM_005969.4	c.*616G>C		3_prime_UTR_variant	16/16	ENST00000380542.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAP1L4	ENST00000380542.9	c.*616G>C		3_prime_UTR_variant	16/16	1	NM_005969.4

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37775 AN: 151350 Hom.: 6373 Cov.: 32

Gnomad AFR AF: 0.0682

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.288

GnomAD4 exome AF: 0.194 AC: 21 AN: 108 Hom.: 4 Cov.: 0 AF XY: 0.162 AC XY: 11 AN XY: 68

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.205

GnomAD4 genome AF: 0.250 AC: 37791 AN: 151456 Hom.: 6387 Cov.: 32 AF XY: 0.254 AC XY: 18810 AN XY: 73976

Gnomad4 AFR AF: 0.0680

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.294

Alfa AF: 0.250 Hom.: 744

Bravo AF: 0.259

Asia WGS AF: 0.480 AC: 1650 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.30
Dann	Benign	0.45

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: rs8505; hg19: chr11-2966293;