chr5-52989287-T-C

Position:

• chr5-52989287-T-C

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+803A>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 0.643 in 671,630 control chromosomes in the GnomAD database, including 138,751 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.65 (29208 hom., cov: 27)
  • Exomes 𝑓: 0.64 (109543 hom.)
• Consequence: ITGA2-AS1 ENST00000662246.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0430

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=-0.64).
• BP6: Variant 5-52989287-T-C is Benign according to our data. Variant chr5-52989287-T-C is described in ClinVar as [Benign]. Clinvar id is 1237373.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.73 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+803A>G		intron_variant, non_coding_transcript_variant
ITGA2-AS1	ENST00000503559.1	n.189+803A>G		intron_variant, non_coding_transcript_variant		5
ITGA2-AS1	ENST00000505701.5	n.189+803A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.646 AC: 93436 AN: 144596 Hom.: 29170 Cov.: 27

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.630

GnomAD4 exome AF: 0.642 AC: 338329 AN: 526932 Hom.: 109543 Cov.: 5 AF XY: 0.648 AC XY: 180485 AN XY: 278470

Gnomad4 AFR exome AF: 0.568

Gnomad4 AMR exome AF: 0.575

Gnomad4 ASJ exome AF: 0.566

Gnomad4 EAS exome AF: 0.534

Gnomad4 SAS exome AF: 0.735

Gnomad4 FIN exome AF: 0.630

Gnomad4 NFE exome AF: 0.655

Gnomad4 OTH exome AF: 0.624

GnomAD4 genome AF: 0.646 AC: 93522 AN: 144698 Hom.: 29208 Cov.: 27 AF XY: 0.648 AC XY: 45782 AN XY: 70702

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.628

Alfa AF: 0.546 Hom.: 1743

Bravo AF: 0.611

Asia WGS AF: 0.609 AC: 2110 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: 26202972, 11313353) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	11
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28095; hg19: chr5-52285117; COSMIC: COSV56859339;