rs11702770

chr21-44924915-A-G

Variant summary

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

The NR_038311.1(ITGB2-AS1):n.388+1932A>G 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 0.268 in 152,060 control chromosomes in the GnomAD database, including 5,595 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 0.27 (5595 hom., cov: 31)
• Consequence: ITGB2-AS1 NR_038311.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

ITGB2-AS1 (HGNC:44304): (ITGB2 antisense RNA 1)

ITGB2 (HGNC:6155): (integrin subunit beta 2) This gene encodes an integrin beta chain, which combines with multiple different alpha chains to form different integrin heterodimers. Integrins are integral cell-surface proteins that participate in cell adhesion as well as cell-surface mediated signalling. The encoded protein plays an important role in immune response and defects in this gene cause leukocyte adhesion deficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITGB2-AS1	NR_038311.1	n.388+1932A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITGB2-AS1	ENST00000441379.5	n.278-1953A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40626 AN: 151942 Hom.: 5574 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.268 AC: 40700 AN: 152060 Hom.: 5595 Cov.: 31 AF XY: 0.265 AC XY: 19691 AN XY: 74316

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.262

Alfa AF: 0.268 Hom.: 1430

Bravo AF: 0.280

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.7
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11702770; hg19: chr21-46344830;