rs3219180

chr6-31549396-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFKBIL1	NM_005007.4	c.334+957C>T		intron_variant		ENST00000376148.9
NFKBIL1	NM_001144961.2	c.334+957C>T		intron_variant
NFKBIL1	NM_001144962.2	c.265+957C>T		intron_variant
NFKBIL1	NM_001144963.2	c.265+957C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFKBIL1	ENST00000376148.9	c.334+957C>T		intron_variant		1	NM_005007.4	P4

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

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0332

Gnomad4 ASJ AF: 0.0831

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0750

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0423

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.43
Dann	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs3219180; hg19: chr6-31517173;