rs1572312

Positions:

• chr1-60952057-G-T

Variant summary

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

The NR_110617.2(NFIA-AS2):​n.773+454C>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 0.0966 in 152,236 control chromosomes in the GnomAD database, including 735 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 0.097 (735 hom., cov: 33)
• Consequence: NFIA-AS2 NR_110617.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIA-AS2	NR_110617.2	n.773+454C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA-AS2	ENST00000655960.1	n.399+36588C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0966 AC: 14696 AN: 152116 Hom.: 735 Cov.: 33

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0705

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0912

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

GnomAD4 genome AF: 0.0966 AC: 14708 AN: 152236 Hom.: 735 Cov.: 33 AF XY: 0.0949 AC XY: 7063 AN XY: 74432

Gnomad4 AFR AF: 0.0891

Gnomad4 AMR AF: 0.0705

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0309

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.102 Hom.: 1155

Bravo AF: 0.0926

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.056
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1572312; hg19: chr1-61417729;