rs2523500

Variant names:

• chr6-31550577-G-A
• rs2523500
• NM_005007.4:c.334+2138G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31550577-G-A
• chr6-31550577-G-C
• chr6-31550577-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.334+2138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 151,990 control chromosomes in the GnomAD database, including 36,035 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 0.69 (36035 hom., cov: 31)
• Consequence: NFKBIL1 NM_005007.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.753 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFKBIL1	NM_005007.4	MANE Select	c.334+2138G>A		intron	N/A	NP_004998.3
	NFKBIL1	NM_001144961.2		c.334+2138G>A		intron	N/A	NP_001138433.1	A0A0A0MRT5
	NFKBIL1	NM_001144962.2		c.265+2138G>A		intron	N/A	NP_001138434.1	Q5STV6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFKBIL1	ENST00000376148.9	TSL:1 MANE Select	c.334+2138G>A		intron	N/A	ENSP00000365318.4	Q9UBC1-1
	NFKBIL1	ENST00000376145.8	TSL:1	c.334+2138G>A		intron	N/A	ENSP00000365315.4	A0A0A0MRT5
	NFKBIL1	ENST00000376146.8	TSL:4	c.265+2138G>A		intron	N/A	ENSP00000365316.4	Q5STV6

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104189 AN: 151872 Hom.: 35993 Cov.: 31

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.686 AC: 104287 AN: 151990 Hom.: 36035 Cov.: 31 AF XY: 0.691 AC XY: 51360 AN XY: 74276

African (AFR) AF: 0.754 AC: 31250 AN: 41470

American (AMR) AF: 0.620 AC: 9466 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2144 AN: 3466

East Asian (EAS) AF: 0.768 AC: 3962 AN: 5160

South Asian (SAS) AF: 0.774 AC: 3728 AN: 4818

European-Finnish (FIN) AF: 0.735 AC: 7755 AN: 10554

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43690 AN: 67938

Other (OTH) AF: 0.684 AC: 1441 AN: 2108

Alfa AF: 0.656 Hom.: 100732

Bravo AF: 0.676

Asia WGS AF: 0.723 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.72
PhyloP100		0.13
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: rs2523500; hg19: chr6-31518354;