1-61016727-G-C

Variant names:

• chr1-61016727-G-C
• rs1779866
• ENST00000371191.5:c.97-71422G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000371191.5(NFIA):​c.97-71422G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,908 control chromosomes in the GnomAD database, including 22,686 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 0.55 (22686 hom., cov: 32)
• Consequence: NFIA ENST00000371191.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 5 publications found

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]

NFIA-AS2 (HGNC:40401): (NFIA antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIA	ENST00000371191.5	c.97-71422G>C		intron_variant	Intron 1 of 10	5		ENSP00000360233.1
NFIA-AS2	ENST00000655960.1	n.272-27955C>G		intron_variant	Intron 1 of 3
NFIA	ENST00000664495.1	n.*119+42776G>C		intron_variant	Intron 2 of 11			ENSP00000499306.1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82777 AN: 151788 Hom.: 22651 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.546 AC: 82866 AN: 151908 Hom.: 22686 Cov.: 32 AF XY: 0.542 AC XY: 40186 AN XY: 74202

African (AFR) AF: 0.515 AC: 21338 AN: 41414

American (AMR) AF: 0.538 AC: 8215 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1721 AN: 3458

East Asian (EAS) AF: 0.478 AC: 2470 AN: 5164

South Asian (SAS) AF: 0.545 AC: 2614 AN: 4800

European-Finnish (FIN) AF: 0.500 AC: 5261 AN: 10516

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39377 AN: 67986

Other (OTH) AF: 0.548 AC: 1152 AN: 2104

Alfa AF: 0.415 Hom.: 1047

Bravo AF: 0.546

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.80
DANN	Benign	0.37
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1779866; hg19: chr1-61482399;