rs11669592

Variant names:

• chr19-3318512-A-G
• rs11669592
• ENST00000641145.1:c.96+3656A>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFIC	ENST00000641145.1	c.96+3656A>G		intron_variant	Intron 1 of 10			ENSP00000492983.1

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;