rs2255798

Variant names:

• chr6-31553525-G-C
• rs2255798
• NM_005007.4:c.335-4103G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31553525-G-C
• chr6-31553525-G-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.335-4103G>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
• Publications: 29 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005007.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFKBIL1	NM_005007.4	MANE Select	c.335-4103G>C		intron	N/A	NP_004998.3
	NFKBIL1	NM_001144961.2		c.335-4103G>C		intron	N/A	NP_001138433.1
	NFKBIL1	NM_001144962.2		c.266-4103G>C		intron	N/A	NP_001138434.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFKBIL1	ENST00000376148.9	TSL:1 MANE Select	c.335-4103G>C		intron	N/A	ENSP00000365318.4
	NFKBIL1	ENST00000376145.8	TSL:1	c.335-4103G>C		intron	N/A	ENSP00000365315.4
	NFKBIL1	ENST00000376146.8	TSL:4	c.266-4103G>C		intron	N/A	ENSP00000365316.4

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

African (AFR) AF: 0.0518 AC: 2148 AN: 41476

American (AMR) AF: 0.104 AC: 1595 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3468

East Asian (EAS) AF: 0.123 AC: 639 AN: 5178

South Asian (SAS) AF: 0.0826 AC: 399 AN: 4828

European-Finnish (FIN) AF: 0.139 AC: 1465 AN: 10556

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.131 AC: 8907 AN: 67964

Other (OTH) AF: 0.115 AC: 242 AN: 2108

Alfa AF: 0.114 Hom.: 155

Bravo AF: 0.102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.59
PhyloP100		0.43
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: rs2255798; hg19: chr6-31521302;