rs2255798

chr6-31553525-G-Cchr6-31553525-G-T

Variant summary

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

The NM_005007.4(NFKBIL1):c.335-4103G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,056 control chromosomes in the GnomAD database, including 963 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 0.10 (963 hom., cov: 31)
• Consequence: NFKBIL1 NM_005007.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFKBIL1	NM_005007.4	c.335-4103G>C		intron_variant		ENST00000376148.9
NFKBIL1	NM_001144961.2	c.335-4103G>C		intron_variant
NFKBIL1	NM_001144962.2	c.266-4103G>C		intron_variant
NFKBIL1	NM_001144963.2	c.266-4103G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFKBIL1	ENST00000376148.9	c.335-4103G>C		intron_variant		1	NM_005007.4	P4

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15867 AN: 151938 Hom.: 965 Cov.: 31

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0828

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.104 AC: 15869 AN: 152056 Hom.: 963 Cov.: 31 AF XY: 0.104 AC XY: 7707 AN XY: 74332

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0826

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.115

Alfa AF: 0.114 Hom.: 155

Bravo AF: 0.102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.8
Dann	Benign	0.59

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: rs2255798; hg19: chr6-31521302;