chr8-93343791-G-A

Variant names:

• chr8-93343791-G-A
• rs7821394
• ENST00000517785.2:n.425+2902C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000517785.2(CIBAR1-DT):​n.425+2902C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,072 control chromosomes in the GnomAD database, including 21,933 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (21933 hom., cov: 33)
• Consequence: CIBAR1-DT ENST00000517785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 5 publications found

Genes affected

CIBAR1-DT (HGNC:43644): (CIBAR1 divergent transcript)

ENSG00000300380 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517785.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIBAR1-DT	ENST00000517785.2	TSL:3	n.425+2902C>T		intron	N/A
	CIBAR1-DT	ENST00000520096.6	TSL:3	n.484+2902C>T		intron	N/A
	CIBAR1-DT	ENST00000520513.2	TSL:3	n.381+2902C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81368 AN: 151952 Hom.: 21926 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.547

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.535 AC: 81414 AN: 152072 Hom.: 21933 Cov.: 33 AF XY: 0.533 AC XY: 39654 AN XY: 74350

African (AFR) AF: 0.557 AC: 23125 AN: 41482

American (AMR) AF: 0.512 AC: 7829 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2211 AN: 3462

East Asian (EAS) AF: 0.347 AC: 1794 AN: 5168

South Asian (SAS) AF: 0.496 AC: 2394 AN: 4822

European-Finnish (FIN) AF: 0.592 AC: 6262 AN: 10574

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35905 AN: 67962

Other (OTH) AF: 0.540 AC: 1141 AN: 2112

Alfa AF: 0.538 Hom.: 12194

Bravo AF: 0.536

Asia WGS AF: 0.456 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7821394; hg19: chr8-94356019;