17-31233782-A-G

Variant summary

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

The NM_001042492.3(NF1):c.3708+569A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,088 control chromosomes in the GnomAD database, including 16,108 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 0.43 (16108 hom., cov: 32)
• Consequence: NF1 NM_001042492.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NF1	NM_001042492.3	c.3708+569A>G		intron_variant		ENST00000358273.9
NF1	NM_000267.3	c.3708+569A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NF1	ENST00000358273.9	c.3708+569A>G		intron_variant		1	NM_001042492.3	P1

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64961 AN: 151970 Hom.: 16087 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.366

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.428 AC: 65030 AN: 152088 Hom.: 16108 Cov.: 32 AF XY: 0.432 AC XY: 32127 AN XY: 74368

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.365

Alfa AF: 0.385 Hom.: 1592

Bravo AF: 0.445

Asia WGS AF: 0.469 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	7.5
Dann	Benign	0.81

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: rs2012581; hg19: chr17-29560800;