8-85463901-A-T

Position:

• chr8-85463901-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NR_121630.1(CA3-AS1):​n.334+681T>A 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 0.984 in 550,414 control chromosomes in the GnomAD database, including 266,647 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.99 (72383 hom., cov: 22)
  • Exomes 𝑓: 0.98 (194264 hom.)
• Consequence: CA3-AS1 NR_121630.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.147

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 8-85463901-A-T is Benign according to our data. Variant chr8-85463901-A-T is described in ClinVar as [Benign]. Clinvar id is 369615.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CA3-AS1	NR_121630.1	n.334+681T>A		intron_variant, non_coding_transcript_variant
CA3-AS1	NR_121631.1	n.106+327T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CA3-AS1	ENST00000521761.6	n.334+681T>A		intron_variant, non_coding_transcript_variant		4
CA3-AS1	ENST00000517697.6	n.193+327T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.986 AC: 146745 AN: 148860 Hom.: 72331 Cov.: 22

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.990

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.991

GnomAD4 exome AF: 0.984 AC: 394950 AN: 401450 Hom.: 194264 Cov.: 5 AF XY: 0.984 AC XY: 218597 AN XY: 222086

Gnomad4 AFR exome AF: 0.994

Gnomad4 AMR exome AF: 0.991

Gnomad4 ASJ exome AF: 0.990

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.993

Gnomad4 FIN exome AF: 0.993

Gnomad4 NFE exome AF: 0.978

Gnomad4 OTH exome AF: 0.985

GnomAD4 genome AF: 0.986 AC: 146849 AN: 148964 Hom.: 72383 Cov.: 22 AF XY: 0.986 AC XY: 71743 AN XY: 72766

Gnomad4 AFR AF: 0.996

Gnomad4 AMR AF: 0.985

Gnomad4 ASJ AF: 0.994

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 0.994

Gnomad4 NFE AF: 0.977

Gnomad4 OTH AF: 0.991

Alfa AF: 0.985 Hom.: 3223

Bravo AF: 0.986

Asia WGS AF: 0.997 AC: 3399 AN: 3410

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Osteopetrosis with renal tubular acidosis Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	16
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11261477; hg19: chr8-86376130;