dbSNP rs11614925: NAP1L1:c.206+105T>C (chr12-76067266-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.187

Publications

4 publications found

Variant links:

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]

NAP1L1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004537.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NAP1L1	NM_004537.7	MANE Select	c.206+105T>C	intron	N/A	NP_004528.1	P55209-1
NAP1L1	NM_001330231.2		c.206+105T>C	intron	N/A	NP_001317160.1	P55209-1
NAP1L1	NM_139207.5		c.206+105T>C	intron	N/A	NP_631946.1	P55209-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NAP1L1	ENST00000618691.5	TSL:1 MANE Select	c.206+105T>C	intron	N/A	ENSP00000477538.1	P55209-1
NAP1L1	ENST00000393263.7	TSL:1	c.206+105T>C	intron	N/A	ENSP00000376947.3	P55209-1
NAP1L1	ENST00000880560.1		c.206+105T>C	intron	N/A	ENSP00000550619.1

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25213

AN:

151972

Hom.:

2259

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.123

AC:

2181

AN:

17770

American (AMR)

AF:

0.143

AC:

4254

AN:

29798

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

3834

AN:

16470

East Asian (EAS)

AF:

0.0281

AC:

989

AN:

35154

South Asian (SAS)

AF:

0.314

AC:

16513

AN:

52630

European-Finnish (FIN)

AF:

0.152

AC:

6092

AN:

40196

Middle Eastern (MID)

AF:

0.334

AC:

784

AN:

2350

European-Non Finnish (NFE)

AF:

0.185

AC:

83281

AN:

448968

Other (OTH)

AF:

0.190

AC:

6214

AN:

32672

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4761

9523

14284

19046

23807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1794

3588

5382

7176

8970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.166

AC:

25222

AN:

152092

Hom.:

2260

Cov.:

AF XY:

0.166

AC XY:

12371

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.122

AC:

5050

AN:

41528

American (AMR)

AF:

0.171

AC:

2619

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.245

AC:

848

AN:

3466

East Asian (EAS)

AF:

0.0362

AC:

188

AN:

5188

South Asian (SAS)

AF:

0.305

AC:

1471

AN:

4816

European-Finnish (FIN)

AF:

0.154

AC:

1634

AN:

10590

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.187

AC:

12710

AN:

67904

Other (OTH)

AF:

0.202

AC:

427

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1081

2163

3244

4326

5407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

282

564

846

1128

1410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.181

Hom.:

6842

Bravo

AF:

0.163

Asia WGS

AF:

0.168

AC:

587

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.9

(source)

DANN

Benign

0.43

PhyloP100

0.19

PromoterAI

-0.0031

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over