1-61406543-GCCCC-GCCCCCCC

Position:

• chr1-61406543-GCCCC-GCCCCCCC

Variant summary

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

The NM_001134673.4(NFIA):​c.1255-7_1255-5dupCCC variant causes a splice region, 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 0.00028 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00018 (0 hom.)
• Consequence: NFIA NM_001134673.4 splice_region, 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]

NFIA (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 18 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFIA	NM_001134673.4	c.1255-7_1255-5dupCCC		splice_region_variant, intron_variant		ENST00000403491.8	NP_001128145.1
NFIA	NM_001145512.2	c.1390-7_1390-5dupCCC		splice_region_variant, intron_variant			NP_001138984.1
NFIA	NM_001145511.2	c.1231-7_1231-5dupCCC		splice_region_variant, intron_variant			NP_001138983.1
NFIA	NM_005595.5	c.1255-7_1255-5dupCCC		splice_region_variant, intron_variant			NP_005586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFIA	ENST00000403491.8	c.1255-7_1255-5dupCCC		splice_region_variant, intron_variant		1	NM_001134673.4	ENSP00000384523.3

Frequencies

GnomAD3 genomes AF: 0.000282 AC: 18 AN: 63828 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000417

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000459

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000357

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000328

Gnomad OTH AF: 0.00122

GnomAD4 exome AF: 0.000177 AC: 144 AN: 813454 Hom.: 0 Cov.: 0 AF XY: 0.000179 AC XY: 73 AN XY: 407128

Gnomad4 AFR exome AF: 0.000108

Gnomad4 AMR exome AF: 0.000242

Gnomad4 ASJ exome AF: 0.000291

Gnomad4 EAS exome AF: 0.000151

Gnomad4 SAS exome AF: 0.000209

Gnomad4 FIN exome AF: 0.000535

Gnomad4 NFE exome AF: 0.000152

Gnomad4 OTH exome AF: 0.000215

GnomAD4 genome AF: 0.000282 AC: 18 AN: 63862 Hom.: 0 Cov.: 0 AF XY: 0.000302 AC XY: 9 AN XY: 29842

Gnomad4 AFR AF: 0.000157

Gnomad4 AMR AF: 0.000417

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000460

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000357

Gnomad4 NFE AF: 0.000328

Gnomad4 OTH AF: 0.00121

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;