chr1-60953520-G-A

Position:

• chr1-60953520-G-A

Variant summary

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

The ENST00000371191.5(NFIA):​c.96+88054G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 152,272 control chromosomes in the GnomAD database, including 563 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 0.075 (563 hom., cov: 33)
• Consequence: NFIA ENST00000371191.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.695

Genes affected

NFIA-AS2 (HGNC:):

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=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFIA-AS2	NR_110617.2	n.599+802C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFIA-AS2	ENST00000438559.5	n.635+802C>T		intron_variant		1
NFIA	ENST00000371191.5	c.96+88054G>A		intron_variant		5		ENSP00000360233.1
NFIA-AS2	ENST00000421455.2	n.1115C>T		non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11430 AN: 152154 Hom.: 563 Cov.: 33

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0610

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0751 AC: 11431 AN: 152272 Hom.: 563 Cov.: 33 AF XY: 0.0736 AC XY: 5482 AN XY: 74440

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.0610

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0863 Hom.: 136

Bravo AF: 0.0683

Asia WGS AF: 0.0680 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17304036; hg19: chr1-61419192;