rs26679

Variant names:

• chr5-52988345-C-G
• rs26679
• ENST00000503559.1:n.190-69G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-52988345-C-G
• chr5-52988345-C-T

Variant summary

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

The ENST00000505701.5(ITGA2-AS1):​n.190-69G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,036 control chromosomes in the GnomAD database, including 29,954 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 0.63 (29954 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ITGA2-AS1 ENST00000505701.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505701.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA2-AS1	NR_186583.1		n.198-69G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITGA2-AS1	ENST00000503559.1	TSL:5	n.190-69G>C		intron	N/A
	ITGA2-AS1	ENST00000505701.5	TSL:4	n.190-69G>C		intron	N/A
	ITGA2-AS1	ENST00000662246.1		n.76-69G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95148 AN: 151918 Hom.: 29911 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.626 AC: 95249 AN: 152036 Hom.: 29954 Cov.: 32 AF XY: 0.628 AC XY: 46694 AN XY: 74314

African (AFR) AF: 0.589 AC: 24400 AN: 41430

American (AMR) AF: 0.602 AC: 9198 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3472

East Asian (EAS) AF: 0.552 AC: 2852 AN: 5164

South Asian (SAS) AF: 0.729 AC: 3514 AN: 4822

European-Finnish (FIN) AF: 0.630 AC: 6660 AN: 10568

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44598 AN: 67978

Other (OTH) AF: 0.609 AC: 1287 AN: 2112

Alfa AF: 0.533 Hom.: 1494

Bravo AF: 0.617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.54
PhyloP100		-0.51

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs26679;

hg19: chr5-52284175;