5-52989247-C-G

Position:

• chr5-52989247-C-G

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+843G>C 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 0.13 in 585,680 control chromosomes in the GnomAD database, including 5,369 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.15 (1685 hom., cov: 32)
  • Exomes 𝑓: 0.12 (3684 hom.)
• Consequence: ITGA2-AS1 ENST00000662246.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.489

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=-0.81).
• BP6: Variant 5-52989247-C-G is Benign according to our data. Variant chr5-52989247-C-G is described in ClinVar as [Benign]. Clinvar id is 1246532.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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+843G>C		intron_variant, non_coding_transcript_variant
ITGA2-AS1	ENST00000503559.1	n.189+843G>C		intron_variant, non_coding_transcript_variant		5
ITGA2-AS1	ENST00000505701.5	n.189+843G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.151 AC: 21154 AN: 139908 Hom.: 1685 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0998

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0915

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.123 AC: 54991 AN: 445678 Hom.: 3684 AF XY: 0.126 AC XY: 29675 AN XY: 234720

Gnomad4 AFR exome AF: 0.200

Gnomad4 AMR exome AF: 0.0753

Gnomad4 ASJ exome AF: 0.104

Gnomad4 EAS exome AF: 0.107

Gnomad4 SAS exome AF: 0.179

Gnomad4 FIN exome AF: 0.0941

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.123

GnomAD4 genome AF: 0.151 AC: 21174 AN: 140002 Hom.: 1685 Cov.: 32 AF XY: 0.151 AC XY: 10277 AN XY: 67856

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0996

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0602 Hom.: 64

Bravo AF: 0.143

Asia WGS AF: 0.170 AC: 589 AN: 3468

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	This variant is associated with the following publications: (PMID: 11313353) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs27646; hg19: chr5-52285077;