8-93290514-C-T

Variant names:

• chr8-93290514-C-T
• rs1374633
• ENST00000517785.2:n.617+12411G>A

Variant summary

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

The ENST00000517785.2(CIBAR1-DT):​n.617+12411G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,216 control chromosomes in the GnomAD database, including 2,855 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 0.18 (2855 hom., cov: 33)
• Consequence: CIBAR1-DT ENST00000517785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 2 publications found

Genes affected

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

ENSG00000254089 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIBAR1-DT	ENST00000517785.2	TSL:3	n.617+12411G>A		intron	N/A
	CIBAR1-DT	ENST00000520096.6	TSL:3	n.676+12411G>A		intron	N/A
	CIBAR1-DT	ENST00000520513.2	TSL:3	n.659+2087G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27779 AN: 152098 Hom.: 2856 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.183 AC: 27790 AN: 152216 Hom.: 2855 Cov.: 33 AF XY: 0.182 AC XY: 13529 AN XY: 74414

African (AFR) AF: 0.101 AC: 4205 AN: 41530

American (AMR) AF: 0.184 AC: 2817 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3472

East Asian (EAS) AF: 0.0888 AC: 460 AN: 5182

South Asian (SAS) AF: 0.173 AC: 833 AN: 4828

European-Finnish (FIN) AF: 0.233 AC: 2475 AN: 10606

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15811 AN: 67992

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.215 Hom.: 6147

Bravo AF: 0.174

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.023
DANN	Benign	0.18
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1374633; hg19: chr8-94302742;