1-61154824-A-G

Variant names:

• chr1-61154824-A-G
• rs334699
• NM_001134673.4:c.559+66144A>G

Variant summary

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

The NM_001134673.4(NFIA):​c.559+66144A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,296 control chromosomes in the GnomAD database, including 65,521 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 0.93 (65521 hom., cov: 33)
• Consequence: NFIA NM_001134673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIA	NM_001134673.4	c.559+66144A>G		intron_variant	Intron 2 of 10	ENST00000403491.8	NP_001128145.1
NFIA	NM_001145512.2	c.694+66144A>G		intron_variant	Intron 3 of 11		NP_001138984.1
NFIA	NM_001145511.2	c.535+66144A>G		intron_variant	Intron 2 of 10		NP_001138983.1
NFIA	NM_005595.5	c.559+66144A>G		intron_variant	Intron 2 of 9		NP_005586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIA	ENST00000403491.8	c.559+66144A>G		intron_variant	Intron 2 of 10	1	NM_001134673.4	ENSP00000384523.3

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140964 AN: 152178 Hom.: 65466 Cov.: 33

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.926 AC: 141078 AN: 152296 Hom.: 65521 Cov.: 33 AF XY: 0.929 AC XY: 69197 AN XY: 74472

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.918

Gnomad4 FIN AF: 0.982

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.941

Alfa AF: 0.940 Hom.: 14789

Bravo AF: 0.922

Asia WGS AF: 0.898 AC: 3122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs334699; hg19: chr1-61620496;