Genetic Variant NF1:c.1393-32T>C (chr17-31214419-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_001042492.3(NF1):c.1393-32T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 1,535,034 control chromosomes in the GnomAD database, including 340,573 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 25785 hom., cov: 31)

Exomes 𝑓: 0.67 ( 314788 hom. )

Consequence

NF1
NM_001042492.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.807

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

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

BP6

Variant 17-31214419-T-C is Benign according to our data. Variant chr17-31214419-T-C is described in ClinVar as [Benign]. Clinvar id is 257276.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
NF1	NM_001042492.3 link	c.1393-32T>C	intron_variant	Intron 12 of 57	ENST00000358273.9	NP_001035957.1	P21359-1
NF1	NM_000267.3 link	c.1393-32T>C	intron_variant	Intron 12 of 56		NP_000258.1	P21359-2
NF1	NM_001128147.3 link	c.1393-32T>C	intron_variant	Intron 12 of 14		NP_001121619.1	P21359-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NF1	ENST00000358273.9 link	c.1393-32T>C		intron_variant	Intron 12 of 57	1	NM_001042492.3	ENSP00000351015.4		P21359-1

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

81601

AN:

151806

Hom.:

25794

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.720

Gnomad AMR

AF:

0.552

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.562

Gnomad SAS

AF:

0.627

Gnomad FIN

AF:

0.656

Gnomad MID

AF:

0.761

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.604

GnomAD3 exomes

AF:

0.620

AC:

149631

AN:

241458

Hom.:

48749

AF XY:

0.636

AC XY:

83694

AN XY:

131550

show subpopulations

Gnomad AFR exome

AF:

0.171

Gnomad AMR exome

AF:

0.502

Gnomad ASJ exome

AF:

0.776

Gnomad EAS exome

AF:

0.559

Gnomad SAS exome

AF:

0.633

Gnomad FIN exome

AF:

0.662

Gnomad NFE exome

AF:

0.697

Gnomad OTH exome

AF:

0.668

GnomAD4 exome

AF:

0.667

AC:

922993

AN:

1383112

Hom.:

314788

Cov.:

AF XY:

0.670

AC XY:

463309

AN XY:

691984

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.509

Gnomad4 ASJ exome

AF:

0.774

Gnomad4 EAS exome

AF:

0.555

Gnomad4 SAS exome

AF:

0.635

Gnomad4 FIN exome

AF:

0.656

Gnomad4 NFE exome

AF:

0.694

Gnomad4 OTH exome

AF:

0.657

GnomAD4 genome

AF:

0.537

AC:

81585

AN:

151922

Hom.:

25785

Cov.:

AF XY:

0.534

AC XY:

39676

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.186

Gnomad4 AMR

AF:

0.552

Gnomad4 ASJ

AF:

0.768

Gnomad4 EAS

AF:

0.561

Gnomad4 SAS

AF:

0.625

Gnomad4 FIN

AF:

0.656

Gnomad4 NFE

AF:

0.704

Gnomad4 OTH

AF:

0.605

Alfa

AF:

0.632

Hom.:

5846

Bravo

AF:

0.517

Asia WGS

AF:

0.565

AC:

1960

AN:

3468

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Neurofibromatosis, type 1

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2025

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 15, 2022

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:2

Jul 06, 2018

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

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

-0.82

CADD

Benign

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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