5-52989268-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.27
Variant links:
Genes affected
ITGA2-AS1 (HGNC:40306): (ITGA2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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-AS1ENST00000662246.1 linkuse as main transcriptn.75+822C>A intron_variant, non_coding_transcript_variant
ITGA2-AS1ENST00000503559.1 linkuse as main transcriptn.189+822C>A intron_variant, non_coding_transcript_variant 5
ITGA2-AS1ENST00000505701.5 linkuse as main transcriptn.189+822C>A intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.0595
AC:
9019
AN:
151620
Hom.:
374
Cov.:
32
show subpopulations
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
show subpopulations
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
show subpopulations
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
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxNov 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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs41308844; hg19: chr5-52285098; API