chr6-31549396-C-T

Variant names:

• chr6-31549396-C-T
• rs3219180
• NM_005007.4:c.334+957C>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+957C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 151,190 control chromosomes in the GnomAD database, including 240 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 0.042 (240 hom., cov: 31)
• Consequence: NFKBIL1 NM_005007.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 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.334+957C>T		intron	N/A	NP_004998.3
	NFKBIL1	NM_001144961.2		c.334+957C>T		intron	N/A	NP_001138433.1
	NFKBIL1	NM_001144962.2		c.265+957C>T		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.334+957C>T		intron	N/A	ENSP00000365318.4
	NFKBIL1	ENST00000376145.8	TSL:1	c.334+957C>T		intron	N/A	ENSP00000365315.4
	NFKBIL1	ENST00000376146.8	TSL:4	c.265+957C>T		intron	N/A	ENSP00000365316.4

Frequencies

GnomAD3 genomes AF: 0.0424 AC: 6399 AN: 151070 Hom.: 240 Cov.: 31

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0332

Gnomad ASJ AF: 0.0831

Gnomad EAS AF: 0.0951

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0750

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0413

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

GnomAD4 genome AF: 0.0424 AC: 6409 AN: 151190 Hom.: 240 Cov.: 31 AF XY: 0.0469 AC XY: 3459 AN XY: 73792

African (AFR) AF: 0.0160 AC: 659 AN: 41156

American (AMR) AF: 0.0332 AC: 501 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.0831 AC: 288 AN: 3466

East Asian (EAS) AF: 0.0949 AC: 490 AN: 5166

South Asian (SAS) AF: 0.156 AC: 740 AN: 4740

European-Finnish (FIN) AF: 0.0750 AC: 784 AN: 10448

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

European-Non Finnish (NFE) AF: 0.0415 AC: 2813 AN: 67806

Other (OTH) AF: 0.0423 AC: 89 AN: 2102

Alfa AF: 0.0410 Hom.: 28

Bravo AF: 0.0347

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.57
PhyloP100		-0.75
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: rs3219180; hg19: chr6-31517173;