rs13192469

Variant names:

• chr6-31559079-T-C
• rs13192469
• NM_005007.4:c.*468T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31559079-T-C
• chr6-31559079-T-G

Variant summary

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

The NM_005007.4(NFKBIL1):​c.*468T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,084 control chromosomes in the GnomAD database, including 247 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 0.043 (247 hom., cov: 31)
• Consequence: NFKBIL1 NM_005007.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 13 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKBIL1	NM_005007.4	c.*468T>C		downstream_gene_variant		ENST00000376148.9	NP_004998.3
NFKBIL1	NM_001144961.2	c.*468T>C		downstream_gene_variant			NP_001138433.1
NFKBIL1	NM_001144962.2	c.*468T>C		downstream_gene_variant			NP_001138434.1
NFKBIL1	NM_001144963.2	c.*468T>C		downstream_gene_variant			NP_001138435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFKBIL1	ENST00000376148.9	c.*468T>C		downstream_gene_variant		1	NM_005007.4	ENSP00000365318.4
NFKBIL1	ENST00000376145.8	c.*468T>C		downstream_gene_variant		1		ENSP00000365315.4
NFKBIL1	ENST00000376146.8	c.*468T>C		downstream_gene_variant		4		ENSP00000365316.4

Frequencies

GnomAD3 genomes AF: 0.0429 AC: 6512 AN: 151966 Hom.: 247 Cov.: 31

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.0956

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0417

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0429 AC: 6522 AN: 152084 Hom.: 247 Cov.: 31 AF XY: 0.0474 AC XY: 3521 AN XY: 74316

African (AFR) AF: 0.0170 AC: 706 AN: 41474

American (AMR) AF: 0.0340 AC: 519 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3468

East Asian (EAS) AF: 0.0954 AC: 493 AN: 5168

South Asian (SAS) AF: 0.156 AC: 749 AN: 4810

European-Finnish (FIN) AF: 0.0758 AC: 802 AN: 10582

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0417 AC: 2833 AN: 67998

Other (OTH) AF: 0.0417 AC: 88 AN: 2108

Alfa AF: 0.0421 Hom.: 470

Bravo AF: 0.0352

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.73
DANN	Benign	0.56
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs13192469; hg19: chr6-31526856;