chr5-52989268-G-T

Position:

• chr5-52989268-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000662246.1(ITGA2-AS1):​n.75+822C>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 0.0672 in 650,998 control chromosomes in the GnomAD database, including 1,921 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.059 (375 hom., cov: 32)
  • Exomes 𝑓: 0.070 (1546 hom.)
• Consequence: ITGA2-AS1 ENST00000662246.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.27

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 5-52989268-G-T is Benign according to our data. Variant chr5-52989268-G-T is described in ClinVar as [Benign]. Clinvar id is 1249583.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0768 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.75+822C>A		intron_variant, non_coding_transcript_variant
ITGA2-AS1	ENST00000503559.1	n.189+822C>A		intron_variant, non_coding_transcript_variant		5
ITGA2-AS1	ENST00000505701.5	n.189+822C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0595 AC: 9019 AN: 151620 Hom.: 374 Cov.: 32

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.0664

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.000389

Gnomad SAS AF: 0.0219

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.0650

GnomAD4 exome AF: 0.0696 AC: 34744 AN: 499266 Hom.: 1546 AF XY: 0.0679 AC XY: 17905 AN XY: 263836

Gnomad4 AFR exome AF: 0.0193

Gnomad4 AMR exome AF: 0.0462

Gnomad4 ASJ exome AF: 0.126

Gnomad4 EAS exome AF: 0.0000323

Gnomad4 SAS exome AF: 0.0241

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.0785

Gnomad4 OTH exome AF: 0.0733

GnomAD4 genome AF: 0.0594 AC: 9017 AN: 151732 Hom.: 375 Cov.: 32 AF XY: 0.0608 AC XY: 4513 AN XY: 74188

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.0561

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.000390

Gnomad4 SAS AF: 0.0221

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0785

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0227 Hom.: 21

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41308844; hg19: chr5-52285098;