Genetic Variant NM_001042492.3:c.4431-46G>C (chr17-31260323-G-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001042492.3(NF1):c.4431-46G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 1,584,532 control chromosomes in the GnomAD database, including 3,718 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.053 ( 276 hom., cov: 32)

Exomes 𝑓: 0.066 ( 3442 hom. )

Consequence

NF1
NM_001042492.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.448

Publications

8 publications found

Variant links:

Genes affected

NF1 (HGNC:7765): (neurofibromin 1) This gene product appears to function as a negative regulator of the ras signal transduction pathway. Mutations in this gene have been linked to neurofibromatosis type 1, juvenile myelomonocytic leukemia and Watson syndrome. The mRNA for this gene is subject to RNA editing (CGA>UGA->Arg1306Term) resulting in premature translation termination. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. [provided by RefSeq, Jul 2008]

NF1 Gene-Disease associations (from GenCC):

neurofibromatosis type 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp
neurofibromatosis-Noonan syndrome
Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp
Moyamoya disease
Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
hereditary pheochromocytoma-paraganglioma
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
familial ovarian cancer
Inheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen

NF1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 17-31260323-G-C is Benign according to our data. Variant chr17-31260323-G-C is described in ClinVar as Benign. ClinVar VariationId is 257290.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0725 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042492.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NF1	NM_001042492.3	MANE Select	c.4431-46G>C		intron	N/A	NP_001035957.1	P21359-1
	NF1	NM_000267.4		c.4368-46G>C		intron	N/A	NP_000258.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NF1	ENST00000358273.9	TSL:1 MANE Select	c.4431-46G>C	intron	N/A	ENSP00000351015.4	P21359-1
NF1	ENST00000356175.7	TSL:1	c.4368-46G>C	intron	N/A	ENSP00000348498.3	P21359-2
NF1	ENST00000579081.6	TSL:1	n.4368-46G>C	intron	N/A	ENSP00000462408.2	J3KSB5

Frequencies

GnomAD3 genomes

AF:

0.0530

AC:

8059

AN:

152130

Hom.:

277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0149

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.0384

Gnomad ASJ

AF:

0.0844

Gnomad EAS

AF:

0.000576

Gnomad SAS

AF:

0.0197

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0742

Gnomad OTH

AF:

0.0588

GnomAD2 exomes

AF:

0.0529

AC:

13203

AN:

249388

AF XY:

0.0541

show subpopulations

Gnomad AFR exome

AF:

0.0124

Gnomad AMR exome

AF:

0.0275

Gnomad ASJ exome

AF:

0.0844

Gnomad EAS exome

AF:

0.0000545

Gnomad FIN exome

AF:

0.101

Gnomad NFE exome

AF:

0.0719

Gnomad OTH exome

AF:

0.0633

GnomAD4 exome

AF:

0.0659

AC:

94351

AN:

1432284

Hom.:

3442

Cov.:

AF XY:

0.0652

AC XY:

46587

AN XY:

714468

show subpopulations

African (AFR)

AF:

0.0116

AC:

380

AN:

32870

American (AMR)

AF:

0.0301

AC:

1343

AN:

44664

Ashkenazi Jewish (ASJ)

AF:

0.0861

AC:

2234

AN:

25942

East Asian (EAS)

AF:

0.000152

AC:

AN:

39488

South Asian (SAS)

AF:

0.0214

AC:

1832

AN:

85510

European-Finnish (FIN)

AF:

0.103

AC:

5288

AN:

51400

Middle Eastern (MID)

AF:

0.0386

AC:

221

AN:

5718

European-Non Finnish (NFE)

AF:

0.0731

AC:

79483

AN:

1087210

Other (OTH)

AF:

0.0599

AC:

3564

AN:

59482

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

4077

8153

12230

16306

20383

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2834

5668

8502

11336

14170

<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:

0.0529

AC:

8059

AN:

152248

Hom.:

276

Cov.:

AF XY:

0.0540

AC XY:

4016

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.0148

AC:

617

AN:

41562

American (AMR)

AF:

0.0383

AC:

586

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0844

AC:

293

AN:

3470

East Asian (EAS)

AF:

0.000578

AC:

AN:

5192

South Asian (SAS)

AF:

0.0197

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.114

AC:

1211

AN:

10590

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0742

AC:

5048

AN:

67992

Other (OTH)

AF:

0.0582

AC:

123

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

381

762

1144

1525

1906

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<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:

0.0433

Hom.:

Bravo

AF:

0.0458

Asia WGS

AF:

0.00837

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Neurofibromatosis, familial spinal (1)

Neurofibromatosis, type 1 (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.4

(source)

DANN

Benign

0.43

PhyloP100

0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=99/1

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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