rs26680

Positions:

• chr5-52988556-T-C

Variant summary

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

The ENST00000662246.1(ITGA2-AS1):​n.76-280A>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 0.805 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 ENST00000662246.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA2-AS1	ENST00000662246.1	n.76-280A>G		intron_variant, non_coding_transcript_variant
ITGA2-AS1	ENST00000503559.1	n.190-280A>G		intron_variant, non_coding_transcript_variant		5
ITGA2-AS1	ENST00000505701.5	n.190-280A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.811

Alfa AF: 0.853 Hom.: 95271

Bravo AF: 0.789

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs26680; hg19: chr5-52284386;