chr1-61406543-GC-G

Position:

• chr1-61406543-GC-G

Variant summary

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

The NM_001134673.4(NFIA):​c.1255-5del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (1080 hom., cov: 0)
  • Exomes 𝑓: 0.099 (960 hom.)
• Consequence: NFIA NM_001134673.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.886

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 1-61406543-GC-G is Benign according to our data. Variant chr1-61406543-GC-G is described in ClinVar as [Benign]. Clinvar id is 1251146.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIA	NM_001134673.4	c.1255-5del		intron_variant		ENST00000403491.8
NFIA	NM_001145511.2	c.1231-5del		intron_variant
NFIA	NM_001145512.2	c.1390-5del		intron_variant
NFIA	NM_005595.5	c.1255-5del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA	ENST00000403491.8	c.1255-5del		intron_variant		1	NM_001134673.4	P1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 8664 AN: 63556 Hom.: 1078 Cov.: 0

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.0370

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.0564

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.116

GnomAD3 exomes AF: 0.162 AC: 8961 AN: 55298 Hom.: 120 AF XY: 0.162 AC XY: 4927 AN XY: 30448

Gnomad AFR exome AF: 0.257

Gnomad AMR exome AF: 0.187

Gnomad ASJ exome AF: 0.228

Gnomad EAS exome AF: 0.205

Gnomad SAS exome AF: 0.181

Gnomad FIN exome AF: 0.113

Gnomad NFE exome AF: 0.131

Gnomad OTH exome AF: 0.156

GnomAD4 exome AF: 0.0993 AC: 79270 AN: 798410 Hom.: 960 Cov.: 0 AF XY: 0.106 AC XY: 42245 AN XY: 398866

Gnomad4 AFR exome AF: 0.246

Gnomad4 AMR exome AF: 0.124

Gnomad4 ASJ exome AF: 0.144

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.155

Gnomad4 FIN exome AF: 0.103

Gnomad4 NFE exome AF: 0.0874

Gnomad4 OTH exome AF: 0.113

GnomAD4 genome AF: 0.136 AC: 8677 AN: 63588 Hom.: 1080 Cov.: 0 AF XY: 0.139 AC XY: 4117 AN XY: 29718

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.0564

Gnomad4 NFE AF: 0.0482

Gnomad4 OTH AF: 0.115

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

Aug 06, 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: rs58081092; hg19: chr1-61872215;