rs11669592

chr19-3318512-A-G

Variant summary

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

The ENST00000641145.1(NFIC):c.96+3656A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,964 control chromosomes in the GnomAD database, including 20,063 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 0.51 (20063 hom., cov: 32)
• Consequence: NFIC ENST00000641145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08

Genes affected

NFIC (HGNC:7786): (nuclear factor I C) The protein encoded by this gene belongs to the CTF/NF-I family. These are dimeric DNA-binding proteins, and function as cellular transcription factors and as replication factors for adenovirus DNA replication. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIC	ENST00000641145.1	c.96+3656A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77156 AN: 151846 Hom.: 20050 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.508 AC: 77196 AN: 151964 Hom.: 20063 Cov.: 32 AF XY: 0.500 AC XY: 37158 AN XY: 74282

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.523

Alfa AF: 0.542 Hom.: 46539

Bravo AF: 0.510

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.20
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11669592; hg19: chr19-3318510;