chr1-61077098-G-GAGGGGAGA

Position:

• chr1-61077098-G-GAGGGGAGA

Variant summary

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

The ENST00000371191.5(NFIA):​c.97-11045_97-11038dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (9936 hom., cov: 0)
• Consequence: NFIA ENST00000371191.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.873

Genes affected

NFIA (HGNC:7784): (nuclear factor I A) This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-61077098-G-GAGGGGAGA is Benign according to our data. Variant chr1-61077098-G-GAGGGGAGA is described in ClinVar as [Benign]. Clinvar id is 1249368.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA	ENST00000371191.5	c.97-11045_97-11038dup		intron_variant		5
NFIA	ENST00000476646.5	c.-114-11045_-114-11038dup		intron_variant		3
NFIA	ENST00000664495.1	c.*120-11045_*120-11038dup		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52116 AN: 151604 Hom.: 9932 Cov.: 0

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.344 AC: 52119 AN: 151722 Hom.: 9936 Cov.: 0 AF XY: 0.341 AC XY: 25306 AN XY: 74120

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.351

Alfa AF: 0.180 Hom.: 289

Asia WGS AF: 0.273 AC: 950 AN: 3478

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

Aug 03, 2018

- -

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: rs71050110; hg19: chr1-61542770;