rs59677118

Positions:

• chr9-14441679-G-A

Variant summary

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

The ENST00000659981.1(ENSG00000287708):​n.417-26921G>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 0.0768 in 151,896 control chromosomes in the GnomAD database, including 574 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 0.077 (574 hom., cov: 31)
• Consequence: ENST00000659981.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFIB	NM_001369458.1	c.96+90268C>T		intron_variant			NP_001356387.1
NFIB	NM_001369459.1	c.96+90268C>T		intron_variant			NP_001356388.1
NFIB	NM_001369462.1	c.96+90268C>T		intron_variant			NP_001356391.1
NFIB	NM_001369468.1	c.96+90268C>T		intron_variant			NP_001356397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000659981.1	n.417-26921G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11656 AN: 151778 Hom.: 573 Cov.: 31

Gnomad AFR AF: 0.0414

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.0667

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

GnomAD4 genome AF: 0.0768 AC: 11665 AN: 151896 Hom.: 574 Cov.: 31 AF XY: 0.0795 AC XY: 5900 AN XY: 74222

Gnomad4 AFR AF: 0.0414

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.0728

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.0892

Gnomad4 OTH AF: 0.0670

Alfa AF: 0.0880 Hom.: 92

Bravo AF: 0.0650

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59677118; hg19: chr9-14441677; COSMIC: COSV60334600;