5-52988556-T-C

Variant names:

• chr5-52988556-T-C
• rs26680
• ENST00000503559.1:n.190-280A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503559.1(ITGA2-AS1):​n.190-280A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,164 control chromosomes in the GnomAD database, including 49,791 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 0.80 (49791 hom., cov: 32)
• Consequence: ITGA2-AS1 ENST00000503559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 8 publications found

Genes affected

ITGA2-AS1 (HGNC:40306): (ITGA2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503559.1. 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
	ITGA2-AS1	NR_186583.1		n.198-280A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA2-AS1	ENST00000503559.1	TSL:5	n.190-280A>G		intron	N/A
	ITGA2-AS1	ENST00000505701.5	TSL:4	n.190-280A>G		intron	N/A
	ITGA2-AS1	ENST00000662246.1		n.76-280A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122372 AN: 152046 Hom.: 49754 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.805 AC: 122469 AN: 152164 Hom.: 49791 Cov.: 32 AF XY: 0.806 AC XY: 59989 AN XY: 74402

African (AFR) AF: 0.696 AC: 28897 AN: 41496

American (AMR) AF: 0.771 AC: 11783 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3060 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3461 AN: 5164

South Asian (SAS) AF: 0.864 AC: 4157 AN: 4814

European-Finnish (FIN) AF: 0.863 AC: 9156 AN: 10606

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.869 AC: 59126 AN: 68004

Other (OTH) AF: 0.811 AC: 1715 AN: 2114

Alfa AF: 0.841 Hom.: 148766

Bravo AF: 0.789

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.52
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs26680; hg19: chr5-52284386;