rs17882240

Positions:

• chr17-31334204-GTGTGAACC-G
• chr17-31334204-GTGTGAACC-GTGTGAACCTGTGAACC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001042492.3(NF1):​c.5813-625_5813-618del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.50 (20360 hom., cov: 0)
• Consequence: NF1 NM_001042492.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.171

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 -10 ACMG points.

• BP6: Variant 17-31334204-GTGTGAACC-G is Benign according to our data. Variant chr17-31334204-GTGTGAACC-G is described in ClinVar as [Benign]. Clinvar id is 1288198.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NF1	NM_001042492.3	c.5813-625_5813-618del		intron_variant		ENST00000358273.9	NP_001035957.1
NF1	NM_000267.3	c.5750-625_5750-618del		intron_variant			NP_000258.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NF1	ENST00000358273.9	c.5813-625_5813-618del		intron_variant		1	NM_001042492.3	ENSP00000351015	P1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 74880 AN: 150916 Hom.: 20354 Cov.: 0

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.594

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.496 AC: 74906 AN: 151030 Hom.: 20360 Cov.: 0 AF XY: 0.493 AC XY: 36352 AN XY: 73714

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.523

Alfa AF: 0.415 Hom.: 1233

Bravo AF: 0.475

Asia WGS AF: 0.435 AC: 1509 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 15, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17882240; hg19: chr17-29661222;