ENST00000654303.1:n.25_32delGGGGCTCC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The ENST00000654303.1(CA3-AS1):​n.25_32delGGGGCTCC 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 0.00266 in 232,476 control chromosomes in the GnomAD database, including 15 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0018 ( 6 hom., cov: 0)
Exomes 𝑓: 0.0042 ( 9 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 Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00177 (259/146666) while in subpopulation SAS AF= 0.0242 (113/4676). AF 95% confidence interval is 0.0206. There are 6 homozygotes in gnomad4. There are 158 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CA3-AS1NR_121630.1 linkn.334+805_334+812delGGGGCTCC intron_variant Intron 1 of 2
CA3-AS1NR_121631.1 linkn.106+451_106+458delGGGGCTCC intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CA3-AS1ENST00000654303.1 linkn.25_32delGGGGCTCC non_coding_transcript_exon_variant Exon 1 of 3
CA3-AS1ENST00000517697.6 linkn.193+451_193+458delGGGGCTCC intron_variant Intron 1 of 2 4
CA3-AS1ENST00000521761.6 linkn.334+805_334+812delGGGGCTCC intron_variant Intron 1 of 2 4

Frequencies

GnomAD3 genomes
AF:
0.00176
AC:
258
AN:
146580
Hom.:
6
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00288
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00107
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0241
Gnomad FIN
AF:
0.000203
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000182
Gnomad OTH
AF:
0.000497
GnomAD4 exome
AF:
0.00418
AC:
359
AN:
85810
Hom.:
9
AF XY:
0.00630
AC XY:
296
AN XY:
47016
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00101
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0219
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000231
Gnomad4 OTH exome
AF:
0.00206
GnomAD4 genome
AF:
0.00177
AC:
259
AN:
146666
Hom.:
6
Cov.:
0
AF XY:
0.00221
AC XY:
158
AN XY:
71514
show subpopulations
Gnomad4 AFR
AF:
0.00289
Gnomad4 AMR
AF:
0.00107
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0242
Gnomad4 FIN
AF:
0.000203
Gnomad4 NFE
AF:
0.000182
Gnomad4 OTH
AF:
0.000491

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