1-61406543-GCCCC-GCCCCCCCC

Position:

• chr1-61406543-GCCCC-GCCCCCCCC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001134673.4(NFIA):​c.1255-8_1255-5dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00014 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000032 (0 hom.)
• Consequence: NFIA NM_001134673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.886

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIA	NM_001134673.4	c.1255-8_1255-5dup		intron_variant		ENST00000403491.8
NFIA	NM_001145511.2	c.1231-8_1231-5dup		intron_variant
NFIA	NM_001145512.2	c.1390-8_1390-5dup		intron_variant
NFIA	NM_005595.5	c.1255-8_1255-5dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA	ENST00000403491.8	c.1255-8_1255-5dup		intron_variant		1	NM_001134673.4	P1

Frequencies

GnomAD3 genomes AF: 0.000141 AC: 9 AN: 63832 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000209

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000357

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000164

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000320 AC: 26 AN: 813516 Hom.: 0 Cov.: 0 AF XY: 0.0000418 AC XY: 17 AN XY: 407158

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000483

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000627

Gnomad4 FIN exome AF: 0.0000892

Gnomad4 NFE exome AF: 0.0000305

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.000141 AC: 9 AN: 63866 Hom.: 0 Cov.: 0 AF XY: 0.000201 AC XY: 6 AN XY: 29850

Gnomad4 AFR AF: 0.000105

Gnomad4 AMR AF: 0.000209

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000357

Gnomad4 NFE AF: 0.000164

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58081092; hg19: chr1-61872215;