rs2207790

Variant names:

• chr1-61432295-G-A
• rs2207790
• NM_001134673.4:c.1512+5739G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-61432295-G-A
• chr1-61432295-G-C
• chr1-61432295-G-T

Variant summary

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

The NM_001134673.4(NFIA):​c.1512+5739G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 147,990 control chromosomes in the GnomAD database, including 13,860 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 0.42 (13860 hom., cov: 26)
• Consequence: NFIA NM_001134673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 13 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 Gene-Disease associations (from GenCC):

• brain malformations with or without urinary tract defects

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
• chromosome 1p32-p31 deletion syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Illumina, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFIA	NM_001134673.4	c.1512+5739G>A		intron_variant	Intron 10 of 10	ENST00000403491.8	NP_001128145.1
NFIA	NM_001145512.2	c.1647+5739G>A		intron_variant	Intron 11 of 11		NP_001138984.1
NFIA	NM_001145511.2	c.1488+5739G>A		intron_variant	Intron 10 of 10		NP_001138983.1
NFIA	NM_005595.5	c.1421-23008G>A		intron_variant	Intron 9 of 9		NP_005586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIA	ENST00000403491.8	c.1512+5739G>A		intron_variant	Intron 10 of 10	1	NM_001134673.4	ENSP00000384523.3

Frequencies

GnomAD3 genomes AF: 0.419 AC: 62007 AN: 147892 Hom.: 13841 Cov.: 26

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.419 AC: 62044 AN: 147990 Hom.: 13860 Cov.: 26 AF XY: 0.428 AC XY: 30802 AN XY: 72040

African (AFR) AF: 0.258 AC: 10224 AN: 39556

American (AMR) AF: 0.392 AC: 5767 AN: 14706

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1244 AN: 3436

East Asian (EAS) AF: 0.438 AC: 2175 AN: 4966

South Asian (SAS) AF: 0.592 AC: 2783 AN: 4700

European-Finnish (FIN) AF: 0.646 AC: 6463 AN: 9998

Middle Eastern (MID) AF: 0.410 AC: 119 AN: 290

European-Non Finnish (NFE) AF: 0.474 AC: 31974 AN: 67390

Other (OTH) AF: 0.432 AC: 882 AN: 2042

Alfa AF: 0.444 Hom.: 37018

Bravo AF: 0.380

Asia WGS AF: 0.531 AC: 1846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.45
DANN	Benign	0.76
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2207790; hg19: chr1-61897967;