rs1909118

chr1-61092333-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001134673.4(NFIA):c.559+3653G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,158 control chromosomes in the GnomAD database, including 3,324 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3324 hom., cov: 32)
• Consequence: NFIA NM_001134673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIA	NM_001134673.4	c.559+3653G>A		intron_variant		ENST00000403491.8
NFIA	NM_001145511.2	c.535+3653G>A		intron_variant
NFIA	NM_001145512.2	c.694+3653G>A		intron_variant
NFIA	NM_005595.5	c.559+3653G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA	ENST00000403491.8	c.559+3653G>A		intron_variant		1	NM_001134673.4	P1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29531 AN: 152038 Hom.: 3302 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.162

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.195 AC: 29598 AN: 152158 Hom.: 3324 Cov.: 32 AF XY: 0.195 AC XY: 14517 AN XY: 74392

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.172

Alfa AF: 0.166 Hom.: 308

Bravo AF: 0.200

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.17
Dann	Benign	0.63

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: rs1909118; hg19: chr1-61558005;