1-61077852-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The ENST00000371191.5(NFIA):c.97-10283del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00599 in 113,358 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0060 (1 hom., cov: 31)
• Consequence: NFIA ENST00000371191.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.959

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 1-61077852-CT-C is Benign according to our data. Variant chr1-61077852-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1214327.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00599 (679/113358) while in subpopulation AFR AF= 0.0165 (517/31302). AF 95% confidence interval is 0.0153. There are 1 homozygotes in gnomad4. There are 304 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High AC in GnomAd at 680 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIA	NM_001145511.2	c.3+238del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA	ENST00000371191.5	c.97-10283del		intron_variant		5
NFIA	ENST00000407417.7	c.3+238del		intron_variant		2
NFIA	ENST00000476646.5	c.-114-10283del		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00600 AC: 680 AN: 113376 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00195

Gnomad ASJ AF: 0.00150

Gnomad EAS AF: 0.00222

Gnomad SAS AF: 0.000290

Gnomad FIN AF: 0.00316

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00189

Gnomad OTH AF: 0.00520

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

GnomAD4 genome AF: 0.00599 AC: 679 AN: 113358 Hom.: 1 Cov.: 31 AF XY: 0.00558 AC XY: 304 AN XY: 54464

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.00195

Gnomad4 ASJ AF: 0.00150

Gnomad4 EAS AF: 0.00223

Gnomad4 SAS AF: 0.000292

Gnomad4 FIN AF: 0.00316

Gnomad4 NFE AF: 0.00189

Gnomad4 OTH AF: 0.00519

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 08, 2019

- -

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: rs1179358669; hg19: chr1-61543524;