rs7189406

Positions:

• chr16-10899631-G-A
• chr16-10899631-G-C
• chr16-10899631-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000246.4(CIITA):​c.436+629G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,104 control chromosomes in the GnomAD database, including 46,602 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 0.75 (46602 hom., cov: 32)
• Consequence: CIITA NM_000246.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.37

Genes affected

CIITA (HGNC:7067): (class II major histocompatibility complex transactivator) This gene encodes a protein with an acidic transcriptional activation domain, 4 LRRs (leucine-rich repeats) and a GTP binding domain. The protein is located in the nucleus and acts as a positive regulator of class II major histocompatibility complex gene transcription, and is referred to as the "master control factor" for the expression of these genes. The protein also binds GTP and uses GTP binding to facilitate its own transport into the nucleus. Once in the nucleus it does not bind DNA but rather uses an intrinsic acetyltransferase (AT) activity to act in a coactivator-like fashion. Mutations in this gene have been associated with bare lymphocyte syndrome type II (also known as hereditary MHC class II deficiency or HLA class II-deficient combined immunodeficiency), increased susceptibility to rheumatoid arthritis, multiple sclerosis, and possibly myocardial infarction. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CIITA	NM_000246.4	c.436+629G>A		intron_variant		ENST00000324288.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIITA	ENST00000324288.14	c.436+629G>A		intron_variant		1	NM_000246.4	P4

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114641 AN: 151986 Hom.: 46600 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.754 AC: 114666 AN: 152104 Hom.: 46602 Cov.: 32 AF XY: 0.749 AC XY: 55689 AN XY: 74368

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.786

Alfa AF: 0.888 Hom.: 51701

Bravo AF: 0.711

Asia WGS AF: 0.677 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.015
DANN	Benign	0.52

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: rs7189406; hg19: chr16-10993488;