chr5-52988345-C-G

Position:

• chr5-52988345-C-G

Variant summary

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

The ENST00000662246.1(ITGA2-AS1):​n.76-69G>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 0.626 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 ENST00000662246.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 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.76-69G>C		intron_variant, non_coding_transcript_variant
ITGA2-AS1	ENST00000503559.1	n.190-69G>C		intron_variant, non_coding_transcript_variant		5
ITGA2-AS1	ENST00000505701.5	n.190-69G>C		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.609

Alfa AF: 0.533 Hom.: 1494

Bravo AF: 0.617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
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: rs26679; hg19: chr5-52284175;