1-61044947-C-T

Variant names:

• chr1-61044947-C-T
• rs1779851
• ENST00000371191.5:c.97-43202C>T

Variant summary

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

The ENST00000371191.5(NFIA):​c.97-43202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,148 control chromosomes in the GnomAD database, including 5,289 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 0.24 (5289 hom., cov: 33)
• Consequence: NFIA ENST00000371191.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIA	ENST00000371191.5	c.97-43202C>T		intron_variant	Intron 1 of 10	5		ENSP00000360233.1
NFIA-AS2	ENST00000655960.1	n.271+11668G>A		intron_variant	Intron 1 of 3
NFIA	ENST00000664495.1	n.*120-43202C>T		intron_variant	Intron 2 of 11			ENSP00000499306.1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36417 AN: 152030 Hom.: 5290 Cov.: 33

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.239 AC: 36411 AN: 152148 Hom.: 5289 Cov.: 33 AF XY: 0.237 AC XY: 17634 AN XY: 74366

African (AFR) AF: 0.0890 AC: 3696 AN: 41526

American (AMR) AF: 0.192 AC: 2928 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3468

East Asian (EAS) AF: 0.135 AC: 700 AN: 5184

South Asian (SAS) AF: 0.307 AC: 1478 AN: 4814

European-Finnish (FIN) AF: 0.287 AC: 3032 AN: 10570

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.335 AC: 22758 AN: 67986

Other (OTH) AF: 0.248 AC: 524 AN: 2114

Alfa AF: 0.298 Hom.: 24253

Bravo AF: 0.224

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.37
PhyloP100		-0.61
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: rs1779851; hg19: chr1-61510619;