chr9-14427729-G-A

Position:

• chr9-14427729-G-A

Variant summary

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

The ENST00000659981.1(ENSG00000287708):​n.416+21241G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0372 in 152,112 control chromosomes in the GnomAD database, including 147 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 0.037 (147 hom., cov: 32)
• Consequence: ENST00000659981.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIB	NM_001369458.1	c.96+104218C>T		intron_variant
NFIB	NM_001369459.1	c.96+104218C>T		intron_variant
NFIB	NM_001369462.1	c.96+104218C>T		intron_variant
NFIB	NM_001369468.1	c.96+104218C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659981.1	n.416+21241G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0373 AC: 5667 AN: 151994 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0212

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.0660

Gnomad SAS AF: 0.0425

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0231

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0372 AC: 5663 AN: 152112 Hom.: 147 Cov.: 32 AF XY: 0.0384 AC XY: 2853 AN XY: 74362

Gnomad4 AFR AF: 0.0618

Gnomad4 AMR AF: 0.0212

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.0654

Gnomad4 SAS AF: 0.0424

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0231

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0277 Hom.: 67

Bravo AF: 0.0375

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs990937; hg19: chr9-14427727;