chr8-85463769-A-AGGAGCCCCGGAGCCCC

Position:

• chr8-85463769-A-AGGAGCCCCGGAGCCCC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00800

Genes affected

CA3-AS1 (HGNC:51657): (CA3 antisense RNA 1)

ACMG classification

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	UniProt
CA3-AS1	NR_121630.1	n.334+812_334+813insGGGGCTCCGGGGCTCC		intron_variant, non_coding_transcript_variant
CA3-AS1	NR_121631.1	n.106+458_106+459insGGGGCTCCGGGGCTCC		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CA3-AS1	ENST00000521761.6	n.334+812_334+813insGGGGCTCCGGGGCTCC		intron_variant, non_coding_transcript_variant		4
CA3-AS1	ENST00000654303.1	n.32_33insGGGGCTCCGGGGCTCC		non_coding_transcript_exon_variant	1/3
CA3-AS1	ENST00000517697.6	n.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

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

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

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

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 07, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs77895131; hg19: chr8-86375998;