NM_001042492.3:c.7458-29G>A

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001042492.3(NF1):c.7458-29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,604,790 control chromosomes in the GnomAD database, including 278,373 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.50 ( 20795 hom., cov: 30)

Exomes 𝑓: 0.59 ( 257578 hom. )

Consequence

NF1
NM_001042492.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 1.23

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 2 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 17-31352228-G-A is Benign according to our data. Variant chr17-31352228-G-A is described in ClinVar as [Benign]. Clinvar id is 257303.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-31352228-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NF1	NM_001042492.3 link	c.7458-29G>A		intron_variant	Intron 50 of 57	ENST00000358273.9	NP_001035957.1	P21359-1
NF1	NM_000267.3 link	c.7395-29G>A		intron_variant	Intron 49 of 56		NP_000258.1	P21359-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NF1	ENST00000358273.9 link	c.7458-29G>A		intron_variant	Intron 50 of 57	1	NM_001042492.3	ENSP00000351015.4		P21359-1

Frequencies

GnomAD3 genomes

AF:

0.501

AC:

75980

AN:

151750

Hom.:

20787

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.677

Gnomad AMR

AF:

0.446

Gnomad ASJ

AF:

0.684

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.568

Gnomad FIN

AF:

0.600

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.620

Gnomad OTH

AF:

0.532

GnomAD3 exomes

AF:

0.535

AC:

133828

AN:

250220

Hom.:

37746

AF XY:

0.552

AC XY:

74658

AN XY:

135286

show subpopulations

Gnomad AFR exome

AF:

0.276

Gnomad AMR exome

AF:

0.376

Gnomad ASJ exome

AF:

0.686

Gnomad EAS exome

AF:

0.354

Gnomad SAS exome

AF:

0.576

Gnomad FIN exome

AF:

0.600

Gnomad NFE exome

AF:

0.611

Gnomad OTH exome

AF:

0.568

GnomAD4 exome

AF:

0.589

AC:

856432

AN:

1452922

Hom.:

257578

Cov.:

AF XY:

0.591

AC XY:

427847

AN XY:

723354

show subpopulations

Gnomad4 AFR exome

AF:

0.272

Gnomad4 AMR exome

AF:

0.387

Gnomad4 ASJ exome

AF:

0.688

Gnomad4 EAS exome

AF:

0.374

Gnomad4 SAS exome

AF:

0.579

Gnomad4 FIN exome

AF:

0.596

Gnomad4 NFE exome

AF:

0.614

Gnomad4 OTH exome

AF:

0.573

GnomAD4 genome

AF:

0.501

AC:

76013

AN:

151868

Hom.:

20795

Cov.:

AF XY:

0.498

AC XY:

36943

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.287

Gnomad4 AMR

AF:

0.445

Gnomad4 ASJ

AF:

0.684

Gnomad4 EAS

AF:

0.356

Gnomad4 SAS

AF:

0.567

Gnomad4 FIN

AF:

0.600

Gnomad4 NFE

AF:

0.620

Gnomad4 OTH

AF:

0.529

Alfa

AF:

0.510

Hom.:

3467

Bravo

AF:

0.478

Asia WGS

AF:

0.441

AC:

1531

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Jul 10, 2018

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Neurofibromatosis, type 1

Benign:2

Feb 01, 2025

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Jun 20, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Neurofibromatosis, familial spinal

Benign:1

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.55

BranchPoint Hunter

2.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over