rs607777

chr1-60933087-G-A

Variant summary

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

The ENST00000655960.1(NFIA-AS2):n.400-18142C>T 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 0.229 in 151,980 control chromosomes in the GnomAD database, including 6,498 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 0.23 (6498 hom., cov: 32)
• Consequence: NFIA-AS2 ENST00000655960.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

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 (AFR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA-AS2	ENST00000655960.1	n.400-18142C>T		intron_variant, non_coding_transcript_variant
NFIA	ENST00000371191.5	c.96+67621G>A		intron_variant		5
NFIA	ENST00000664495.1	c.97-40659G>A		intron_variant, NMD_transcript_variant
NFIA-AS2	ENST00000665665.1	n.2312-18142C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34784 AN: 151862 Hom.: 6470 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.229 AC: 34872 AN: 151980 Hom.: 6498 Cov.: 32 AF XY: 0.232 AC XY: 17219 AN XY: 74302

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.0959

Gnomad4 OTH AF: 0.185

Alfa AF: 0.118 Hom.: 2407

Bravo AF: 0.242

Asia WGS AF: 0.233 AC: 810 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	0.74
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs607777; hg19: chr1-61398759;