6-31557074-C-T

Variant names:

• chr6-31557074-C-T
• rs2857605
• NM_005007.4:c.335-554C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005007.4(NFKBIL1):​c.335-554C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 151,610 control chromosomes in the GnomAD database, including 53,372 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 0.84 (53372 hom., cov: 29)
• Consequence: NFKBIL1 NM_005007.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 57 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKBIL1	NM_005007.4	c.335-554C>T		intron_variant	Intron 2 of 3	ENST00000376148.9	NP_004998.3
NFKBIL1	NM_001144961.2	c.335-554C>T		intron_variant	Intron 2 of 3		NP_001138433.1
NFKBIL1	NM_001144962.2	c.266-554C>T		intron_variant	Intron 2 of 3		NP_001138434.1
NFKBIL1	NM_001144963.2	c.266-554C>T		intron_variant	Intron 2 of 3		NP_001138435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFKBIL1	ENST00000376148.9	c.335-554C>T		intron_variant	Intron 2 of 3	1	NM_005007.4	ENSP00000365318.4

Frequencies

GnomAD3 genomes AF: 0.837 AC: 126768 AN: 151494 Hom.: 53319 Cov.: 29

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.837 AC: 126880 AN: 151610 Hom.: 53372 Cov.: 29 AF XY: 0.836 AC XY: 61840 AN XY: 74014

African (AFR) AF: 0.918 AC: 37882 AN: 41280

American (AMR) AF: 0.867 AC: 13212 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3073 AN: 3472

East Asian (EAS) AF: 0.834 AC: 4303 AN: 5160

South Asian (SAS) AF: 0.783 AC: 3765 AN: 4810

European-Finnish (FIN) AF: 0.764 AC: 7928 AN: 10372

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53850 AN: 67966

Other (OTH) AF: 0.864 AC: 1823 AN: 2110

Alfa AF: 0.814 Hom.: 206782

Bravo AF: 0.852

Asia WGS AF: 0.763 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.77
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2857605; hg19: chr6-31524851;