chr8-85463769-A-AGGAGCCCC

Position:

• chr8-85463769-A-AGGAGCCCC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NR_121630.1(CA3-AS1):​n.334+812_334+813insGGGGCTCC 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 0.502 in 231,744 control chromosomes in the GnomAD database, including 33,341 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.57 (24746 hom., cov: 0)
  • Exomes 𝑓: 0.38 (8595 hom.)
• Consequence: CA3-AS1 NR_121630.1 intron, non_coding_transcript
• Clinical Significance: 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-AGGAGCCCC is Benign according to our data. Variant chr8-85463769-A-AGGAGCCCC is described in ClinVar as [Benign]. Clinvar id is 1225462.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA3-AS1	NR_121630.1	n.334+812_334+813insGGGGCTCC		intron_variant, non_coding_transcript_variant
CA3-AS1	NR_121631.1	n.106+458_106+459insGGGGCTCC		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+813insGGGGCTCC		intron_variant, non_coding_transcript_variant		4
CA3-AS1	ENST00000654303.1	n.32_33insGGGGCTCC		non_coding_transcript_exon_variant	1/3
CA3-AS1	ENST00000517697.6	n.193+458_193+459insGGGGCTCC		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.574 AC: 84047 AN: 146442 Hom.: 24730 Cov.: 0

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.587

GnomAD4 exome AF: 0.380 AC: 32354 AN: 85216 Hom.: 8595 AF XY: 0.367 AC XY: 17148 AN XY: 46706

Gnomad4 AFR exome AF: 0.356

Gnomad4 AMR exome AF: 0.200

Gnomad4 ASJ exome AF: 0.306

Gnomad4 EAS exome AF: 0.0666

Gnomad4 SAS exome AF: 0.308

Gnomad4 FIN exome AF: 0.483

Gnomad4 NFE exome AF: 0.424

Gnomad4 OTH exome AF: 0.382

GnomAD4 genome AF: 0.574 AC: 84090 AN: 146528 Hom.: 24746 Cov.: 0 AF XY: 0.576 AC XY: 41147 AN XY: 71450

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.587

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 11, 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;