chr1-61079500-A-G

Position:

• chr1-61079500-A-G

Variant summary

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

The NM_001145511.2(NFIA):​c.3+1872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0844 in 152,278 control chromosomes in the GnomAD database, including 612 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 0.084 (612 hom., cov: 33)
• Consequence: NFIA NM_001145511.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.64

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFIA	NM_001145511.2	c.3+1872A>G		intron_variant			NP_001138983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFIA	ENST00000371191.5	c.97-8649A>G		intron_variant		5		ENSP00000360233
NFIA	ENST00000407417.7	c.3+1872A>G		intron_variant		2		ENSP00000384680
NFIA	ENST00000476646.5	c.-114-8649A>G		intron_variant		3		ENSP00000474461

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12835 AN: 152160 Hom.: 605 Cov.: 33

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.0844 AC: 12855 AN: 152278 Hom.: 612 Cov.: 33 AF XY: 0.0834 AC XY: 6210 AN XY: 74458

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.0857

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.0957 Hom.: 324

Bravo AF: 0.0826

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	20
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12130085; hg19: chr1-61545172;