chr1-61082672-TTC-T

Position:

• chr1-61082672-TTC-T

Variant summary

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

The NM_001134673.4(NFIA):​c.-96_-95del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 142,040 control chromosomes in the GnomAD database, including 82 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.024 (82 hom., cov: 27)
  • Exomes 𝑓: 0.27 (19 hom.)
  • Failed GnomAD Quality Control
• Consequence: NFIA NM_001134673.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.156

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 1-61082672-TTC-T is Benign according to our data. Variant chr1-61082672-TTC-T is described in ClinVar as [Benign]. Clinvar id is 1295689.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIA	NM_001134673.4	c.-96_-95del		5_prime_UTR_variant	1/11	ENST00000403491.8
NFIA	NM_005595.5	c.-96_-95del		5_prime_UTR_variant	1/10
NFIA	NM_001145511.2	c.3+5068_3+5069del		intron_variant
NFIA	NM_001145512.2	c.105-65_105-64del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA	ENST00000403491.8	c.-96_-95del		5_prime_UTR_variant	1/11	1	NM_001134673.4	P1

Frequencies

GnomAD3 genomes AF: 0.0239 AC: 3390 AN: 141996 Hom.: 81 Cov.: 27

Gnomad AFR AF: 0.0603

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.00362

Gnomad EAS AF: 0.0348

Gnomad SAS AF: 0.0163

Gnomad FIN AF: 0.0177

Gnomad MID AF: 0.00690

Gnomad NFE AF: 0.00319

Gnomad OTH AF: 0.0165

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.269 AC: 240048 AN: 893154 Hom.: 19 AF XY: 0.276 AC XY: 121521 AN XY: 440946

Gnomad4 AFR exome AF: 0.279

Gnomad4 AMR exome AF: 0.292

Gnomad4 ASJ exome AF: 0.314

Gnomad4 EAS exome AF: 0.334

Gnomad4 SAS exome AF: 0.323

Gnomad4 FIN exome AF: 0.355

Gnomad4 NFE exome AF: 0.256

Gnomad4 OTH exome AF: 0.283

GnomAD4 genome AF: 0.0239 AC: 3399 AN: 142040 Hom.: 82 Cov.: 27 AF XY: 0.0245 AC XY: 1690 AN XY: 68986

Gnomad4 AFR AF: 0.0604

Gnomad4 AMR AF: 0.0285

Gnomad4 ASJ AF: 0.00362

Gnomad4 EAS AF: 0.0345

Gnomad4 SAS AF: 0.0159

Gnomad4 FIN AF: 0.0177

Gnomad4 NFE AF: 0.00321

Gnomad4 OTH AF: 0.0169

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

Oct 21, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs113913435; hg19: chr1-61548344;