rs9302456

Positions:

• chr16-10874615-C-T

Variant summary

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

The ENST00000572017.1(ENSG00000262151):​n.439-9565G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,160 control chromosomes in the GnomAD database, including 6,102 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 0.26 (6102 hom., cov: 32)
• Consequence: ENST00000572017.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

Genes affected

(HGNC:):

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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CIITA	XM_006720880.4	c.346+8043C>T		intron_variant			XP_006720943.2
CIITA	XM_011522484.4	c.346+8043C>T		intron_variant			XP_011520786.1
CIITA	XM_011522485.3	c.346+8043C>T		intron_variant			XP_011520787.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000572017.1	n.439-9565G>A		intron_variant, non_coding_transcript_variant		3
CIITA	ENST00000636238.1	c.-21+8296C>T		intron_variant		5		ENSP00000490205
CIITA	ENST00000637439.1	c.283+8043C>T		intron_variant		5		ENSP00000489907

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39448 AN: 152042 Hom.: 6103 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.0851

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.259 AC: 39452 AN: 152160 Hom.: 6102 Cov.: 32 AF XY: 0.261 AC XY: 19383 AN XY: 74382

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.0853

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.288

Alfa AF: 0.316 Hom.: 7543

Bravo AF: 0.239

Asia WGS AF: 0.253 AC: 880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.5
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9302456; hg19: chr16-10968472;