rs10961534

chr9-14470835-A-G

Variant summary

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

The ENST00000659981.1(ENSG00000287708):n.2652A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,154 control chromosomes in the GnomAD database, including 1,757 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 0.14 (1757 hom., cov: 33)
• Consequence: ENST00000659981.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIB	NM_001369458.1	c.96+61112T>C		intron_variant
NFIB	NM_001369459.1	c.96+61112T>C		intron_variant
NFIB	NM_001369462.1	c.96+61112T>C		intron_variant
NFIB	NM_001369468.1	c.96+61112T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659981.1	n.2652A>G		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21478 AN: 152036 Hom.: 1757 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.0880

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.141 AC: 21498 AN: 152154 Hom.: 1757 Cov.: 33 AF XY: 0.138 AC XY: 10294 AN XY: 74412

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.0891

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.155

Alfa AF: 0.121 Hom.: 2802

Bravo AF: 0.151

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.30
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10961534; hg19: chr9-14470833;