1-61081568-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000371191.5(NFIA):​c.97-6581A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00357 in 152,262 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0036 ( 3 hom., cov: 31)

Consequence

NFIA
ENST00000371191.5 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.05
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.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 1-61081568-A-G is Benign according to our data. Variant chr1-61081568-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1223209.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 544 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NFIANM_001145511.2 linkuse as main transcriptc.3+3940A>G intron_variant NP_001138983.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NFIAENST00000371191.5 linkuse as main transcriptc.97-6581A>G intron_variant 5 ENSP00000360233
NFIAENST00000407417.7 linkuse as main transcriptc.3+3940A>G intron_variant 2 ENSP00000384680 Q12857-3
NFIAENST00000476646.5 linkuse as main transcriptc.-114-6581A>G intron_variant 3 ENSP00000474461

Frequencies

GnomAD3 genomes
AF:
0.00356
AC:
542
AN:
152144
Hom.:
3
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0125
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0000882
Gnomad OTH
AF:
0.00191
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00357
AC:
544
AN:
152262
Hom.:
3
Cov.:
31
AF XY:
0.00369
AC XY:
275
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.0125
Gnomad4 AMR
AF:
0.000719
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000882
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.00250
Hom.:
0
Bravo
AF:
0.00381
Asia WGS
AF:
0.00115
AC:
4
AN:
3478

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 testingGeneDxAug 20, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
CADD
Benign
16
DANN
Benign
0.83

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: rs140250340; hg19: chr1-61547240; API