rs1779851

Positions:

• chr1-61044947-C-T

Variant summary

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

The ENST00000655960.1(NFIA-AS2):​n.271+11668G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,148 control chromosomes in the GnomAD database, including 5,289 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 0.24 (5289 hom., cov: 33)
• Consequence: NFIA-AS2 ENST00000655960.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

Genes affected

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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFIA-AS2	ENST00000655960.1	n.271+11668G>A		intron_variant, non_coding_transcript_variant
NFIA	ENST00000371191.5	c.97-43202C>T		intron_variant		5		ENSP00000360233
NFIA	ENST00000664495.1	c.*120-43202C>T		intron_variant, NMD_transcript_variant				ENSP00000499306

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36417 AN: 152030 Hom.: 5290 Cov.: 33

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.239 AC: 36411 AN: 152148 Hom.: 5289 Cov.: 33 AF XY: 0.237 AC XY: 17634 AN XY: 74366

Gnomad4 AFR AF: 0.0890

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.248

Alfa AF: 0.310 Hom.: 10400

Bravo AF: 0.224

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1779851; hg19: chr1-61510619;