chr1-61082594-CGCTG-C

Position:

• chr1-61082594-CGCTG-C

Variant summary

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

The NM_001134673.4(NFIA):​c.-185_-182del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00548 in 1,486,512 control chromosomes in the GnomAD database, including 184 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.020 (79 hom., cov: 28)
  • Exomes 𝑓: 0.0039 (105 hom.)
• Consequence: NFIA NM_001134673.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

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 1-61082594-CGCTG-C is Benign according to our data. Variant chr1-61082594-CGCTG-C is described in ClinVar as [Benign]. Clinvar id is 1296107.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFIA	NM_001134673.4	c.-185_-182del		5_prime_UTR_variant	1/11	ENST00000403491.8	NP_001128145.1
NFIA	NM_005595.5	c.-185_-182del		5_prime_UTR_variant	1/10		NP_005586.1
NFIA	NM_001145511.2	c.3+4979_3+4982del		intron_variant			NP_001138983.1
NFIA	NM_001145512.2	c.105-154_105-151del		intron_variant			NP_001138984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFIA	ENST00000403491.8	c.-185_-182del		5_prime_UTR_variant	1/11	1	NM_001134673.4	ENSP00000384523	P1

Frequencies

GnomAD3 genomes AF: 0.0196 AC: 2942 AN: 150448 Hom.: 80 Cov.: 28

Gnomad AFR AF: 0.0557

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0242

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0342

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000371

Gnomad OTH AF: 0.0115

GnomAD4 exome AF: 0.00390 AC: 5206 AN: 1335954 Hom.: 105 AF XY: 0.00386 AC XY: 2520 AN XY: 652798

Gnomad4 AFR exome AF: 0.0563

Gnomad4 AMR exome AF: 0.0298

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0311

Gnomad4 SAS exome AF: 0.0117

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000191

Gnomad4 OTH exome AF: 0.00940

GnomAD4 genome AF: 0.0195 AC: 2943 AN: 150558 Hom.: 79 Cov.: 28 AF XY: 0.0199 AC XY: 1466 AN XY: 73596

Gnomad4 AFR AF: 0.0557

Gnomad4 AMR AF: 0.0242

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0339

Gnomad4 SAS AF: 0.0153

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000371

Gnomad4 OTH AF: 0.0119

Bravo AF: 0.0234

Asia WGS AF: 0.0470 AC: 163 AN: 3466

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

May 18, 2021

- -

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: rs143384586; hg19: chr1-61548266;