1-61077852-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

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

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.959
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 GnomAd4 at 679 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NFIANM_001145511.2 linkuse as main transcriptc.3+238del intron_variant NP_001138983.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NFIAENST00000371191.5 linkuse as main transcriptc.97-10283del intron_variant 5 ENSP00000360233
NFIAENST00000407417.7 linkuse as main transcriptc.3+238del intron_variant 2 ENSP00000384680 Q12857-3
NFIAENST00000476646.5 linkuse as main transcriptc.-114-10283del intron_variant 3 ENSP00000474461

Frequencies

GnomAD3 genomes
AF:
0.00600
AC:
680
AN:
113376
Hom.:
1
Cov.:
31
show subpopulations
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
show subpopulations
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
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxSep 08, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs1179358669; hg19: chr1-61543524; API