chr8-85463769-A-AGGAGCCCCGGAGCCCC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NR_121630.1(CA3-AS1):​n.334+812_334+813insGGGGCTCCGGGGCTCC 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 0.0256 in 232,340 control chromosomes in the GnomAD database, including 132 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.029 ( 99 hom., cov: 0)
Exomes 𝑓: 0.020 ( 33 hom. )

Consequence

CA3-AS1
NR_121630.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00800
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 Benign. Variant got -10 ACMG points.

BP6
Variant 8-85463769-A-AGGAGCCCCGGAGCCCC is Benign according to our data. Variant chr8-85463769-A-AGGAGCCCCGGAGCCCC is described in ClinVar as [Likely_benign]. Clinvar id is 1190097.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0289 (4234/146648) while in subpopulation NFE AF= 0.0456 (3011/65968). AF 95% confidence interval is 0.0443. There are 99 homozygotes in gnomad4. There are 1924 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 99 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CA3-AS1NR_121630.1 linkuse as main transcriptn.334+812_334+813insGGGGCTCCGGGGCTCC intron_variant, non_coding_transcript_variant
CA3-AS1NR_121631.1 linkuse as main transcriptn.106+458_106+459insGGGGCTCCGGGGCTCC intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CA3-AS1ENST00000521761.6 linkuse as main transcriptn.334+812_334+813insGGGGCTCCGGGGCTCC intron_variant, non_coding_transcript_variant 4
CA3-AS1ENST00000654303.1 linkuse as main transcriptn.32_33insGGGGCTCCGGGGCTCC non_coding_transcript_exon_variant 1/3
CA3-AS1ENST00000517697.6 linkuse as main transcriptn.193+458_193+459insGGGGCTCCGGGGCTCC intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.0289
AC:
4238
AN:
146562
Hom.:
100
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00916
Gnomad AMI
AF:
0.00455
Gnomad AMR
AF:
0.0297
Gnomad ASJ
AF:
0.0214
Gnomad EAS
AF:
0.000415
Gnomad SAS
AF:
0.0130
Gnomad FIN
AF:
0.0208
Gnomad MID
AF:
0.0207
Gnomad NFE
AF:
0.0457
Gnomad OTH
AF:
0.0333
GnomAD4 exome
AF:
0.0201
AC:
1722
AN:
85692
Hom.:
33
AF XY:
0.0191
AC XY:
895
AN XY:
46936
show subpopulations
Gnomad4 AFR exome
AF:
0.00414
Gnomad4 AMR exome
AF:
0.00806
Gnomad4 ASJ exome
AF:
0.0115
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00812
Gnomad4 FIN exome
AF:
0.0153
Gnomad4 NFE exome
AF:
0.0267
Gnomad4 OTH exome
AF:
0.0208
GnomAD4 genome
AF:
0.0289
AC:
4234
AN:
146648
Hom.:
99
Cov.:
0
AF XY:
0.0269
AC XY:
1924
AN XY:
71506
show subpopulations
Gnomad4 AFR
AF:
0.00913
Gnomad4 AMR
AF:
0.0296
Gnomad4 ASJ
AF:
0.0214
Gnomad4 EAS
AF:
0.000417
Gnomad4 SAS
AF:
0.0128
Gnomad4 FIN
AF:
0.0208
Gnomad4 NFE
AF:
0.0456
Gnomad4 OTH
AF:
0.0329

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 07, 2020- -

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