ENST00000654303.1:n.17_32delGGGGCTCCGGGGCTCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000654303.1(CA3-AS1):​n.17_32delGGGGCTCCGGGGCTCC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000559 in 232,482 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000055 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000058 ( 0 hom. )

Consequence

CA3-AS1
ENST00000654303.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.28
Variant links:
Genes affected
CA3-AS1 (HGNC:51657): (CA3 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CA3-AS1NR_121630.1 linkn.334+797_334+812delGGGGCTCCGGGGCTCC intron_variant Intron 1 of 2
CA3-AS1NR_121631.1 linkn.106+443_106+458delGGGGCTCCGGGGCTCC intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CA3-AS1ENST00000654303.1 linkn.17_32delGGGGCTCCGGGGCTCC non_coding_transcript_exon_variant Exon 1 of 3
CA3-AS1ENST00000517697.6 linkn.193+443_193+458delGGGGCTCCGGGGCTCC intron_variant Intron 1 of 2 4
CA3-AS1ENST00000521761.6 linkn.334+797_334+812delGGGGCTCCGGGGCTCC intron_variant Intron 1 of 2 4

Frequencies

GnomAD3 genomes
AF:
0.0000546
AC:
8
AN:
146586
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000252
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000623
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000606
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000583
AC:
5
AN:
85810
Hom.:
0
AF XY:
0.0000213
AC XY:
1
AN XY:
47016
show subpopulations
Gnomad4 AFR exome
AF:
0.00104
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000654
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000577
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000545
AC:
8
AN:
146672
Hom.:
0
Cov.:
0
AF XY:
0.0000559
AC XY:
4
AN XY:
71516
show subpopulations
Gnomad4 AFR
AF:
0.0000252
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000625
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000606
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs77895131; hg19: chr8-86375998; API