rs766488

chr1-61344843-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.701-7607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,006 control chromosomes in the GnomAD database, including 10,700 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 0.36 (10700 hom., cov: 32)
• Consequence: NFIA NM_001134673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.858

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIA	NM_001134673.4	c.701-7607G>A		intron_variant		ENST00000403491.8
NFIA	NM_001145511.2	c.677-7607G>A		intron_variant
NFIA	NM_001145512.2	c.836-7607G>A		intron_variant
NFIA	NM_005595.5	c.701-7607G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA	ENST00000403491.8	c.701-7607G>A		intron_variant		1	NM_001134673.4	P1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54634 AN: 151888 Hom.: 10685 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.360 AC: 54700 AN: 152006 Hom.: 10700 Cov.: 32 AF XY: 0.359 AC XY: 26653 AN XY: 74292

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.0856

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.354

Alfa AF: 0.323 Hom.: 11799

Bravo AF: 0.361

Asia WGS AF: 0.172 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	8.4
Dann	Benign	0.60

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: rs766488; hg19: chr1-61810515;