6-31557542-C-T

Position:

• chr6-31557542-C-T

Variant summary

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

The ENST00000376148.9(NFKBIL1):​c.335-86C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 1,089,910 control chromosomes in the GnomAD database, including 269,884 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 0.74 (42735 hom., cov: 32)
  • Exomes 𝑓: 0.69 (227149 hom.)
• Consequence: NFKBIL1 ENST00000376148.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

NFKBIL1 (HGNC:7800): (NFKB inhibitor like 1) This gene encodes a divergent member of the I-kappa-B family of proteins. Its function has not been determined. The gene lies within the major histocompatibility complex (MHC) class I region on chromosome 6. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2009]

NFKBIL1 (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 (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFKBIL1	NM_005007.4	c.335-86C>T		intron_variant		ENST00000376148.9	NP_004998.3
NFKBIL1	NM_001144961.2	c.335-86C>T		intron_variant			NP_001138433.1
NFKBIL1	NM_001144962.2	c.266-86C>T		intron_variant			NP_001138434.1
NFKBIL1	NM_001144963.2	c.266-86C>T		intron_variant			NP_001138435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFKBIL1	ENST00000376148.9	c.335-86C>T		intron_variant		1	NM_005007.4	ENSP00000365318.4

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112987 AN: 151942 Hom.: 42686 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.760

GnomAD4 exome AF: 0.694 AC: 651010 AN: 937850 Hom.: 227149 AF XY: 0.694 AC XY: 323919 AN XY: 466502

Gnomad4 AFR exome AF: 0.881

Gnomad4 AMR exome AF: 0.767

Gnomad4 ASJ exome AF: 0.768

Gnomad4 EAS exome AF: 0.659

Gnomad4 SAS exome AF: 0.712

Gnomad4 FIN exome AF: 0.634

Gnomad4 NFE exome AF: 0.688

Gnomad4 OTH exome AF: 0.704

GnomAD4 genome AF: 0.744 AC: 113101 AN: 152060 Hom.: 42735 Cov.: 32 AF XY: 0.742 AC XY: 55110 AN XY: 74292

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.761

Alfa AF: 0.700 Hom.: 59182

Bravo AF: 0.761

Asia WGS AF: 0.673 AC: 2339 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	3.9
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2239707; hg19: chr6-31525319;