1-60890848-G-T

Position:

• chr1-60890848-G-T

Variant summary

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

The ENST00000371191.5(NFIA):​c.96+25382G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,188 control chromosomes in the GnomAD database, including 960 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 0.11 (960 hom., cov: 32)
• Consequence: NFIA ENST00000371191.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFIA	ENST00000371191.5	c.96+25382G>T		intron_variant		5		ENSP00000360233
NFIA	ENST00000664495.1	c.96+25382G>T		intron_variant, NMD_transcript_variant				ENSP00000499306

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16699 AN: 152070 Hom.: 956 Cov.: 32

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.110 AC: 16717 AN: 152188 Hom.: 960 Cov.: 32 AF XY: 0.110 AC XY: 8203 AN XY: 74414

Gnomad4 AFR AF: 0.0702

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.112

Alfa AF: 0.108 Hom.: 560

Bravo AF: 0.111

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12122228; hg19: chr1-61356520;