chr1-60933087-G-A

Variant names:

• chr1-60933087-G-A
• rs607777
• ENST00000371191.5:c.96+67621G>A

Variant summary

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

The ENST00000371191.5(NFIA):​c.96+67621G>A variant causes a intron 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 ENST00000371191.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371191.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFIA	ENST00000371191.5	TSL:5	c.96+67621G>A		intron	N/A	ENSP00000360233.1
	NFIA-AS2	ENST00000655960.1		n.400-18142C>T		intron	N/A
	NFIA	ENST00000664495.1		n.97-40659G>A		intron	N/A	ENSP00000499306.1

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

African (AFR) AF: 0.512 AC: 21195 AN: 41366

American (AMR) AF: 0.188 AC: 2871 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3470

East Asian (EAS) AF: 0.183 AC: 947 AN: 5176

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4810

European-Finnish (FIN) AF: 0.146 AC: 1544 AN: 10562

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.0959 AC: 6519 AN: 67994

Other (OTH) AF: 0.185 AC: 389 AN: 2108

Alfa AF: 0.134 Hom.: 4502

Bravo AF: 0.242

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.74
DANN	Benign	0.88
PhyloP100		-0.33
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: rs607777; hg19: chr1-61398759;