8-93345870-G-T

Variant names:

• chr8-93345870-G-T
• rs7387468
• ENST00000517785.2:n.425+823C>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.425+823C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,412 control chromosomes in the GnomAD database, including 21,853 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 (21853 hom., cov: 31)
• Consequence: CIBAR1-DT ENST00000517785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 6 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=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIBAR1-DT	ENST00000517785.2	n.425+823C>A		intron_variant	Intron 2 of 5	3
CIBAR1-DT	ENST00000520096.6	n.484+823C>A		intron_variant	Intron 3 of 5	3
CIBAR1-DT	ENST00000520513.2	n.381+823C>A		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81121 AN: 151292 Hom.: 21844 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.591

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.536 AC: 81168 AN: 151412 Hom.: 21853 Cov.: 31 AF XY: 0.534 AC XY: 39524 AN XY: 73984

African (AFR) AF: 0.560 AC: 23093 AN: 41202

American (AMR) AF: 0.512 AC: 7792 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2215 AN: 3468

East Asian (EAS) AF: 0.346 AC: 1767 AN: 5108

South Asian (SAS) AF: 0.495 AC: 2374 AN: 4792

European-Finnish (FIN) AF: 0.593 AC: 6237 AN: 10518

Middle Eastern (MID) AF: 0.590 AC: 170 AN: 288

European-Non Finnish (NFE) AF: 0.528 AC: 35816 AN: 67810

Other (OTH) AF: 0.541 AC: 1135 AN: 2098

Alfa AF: 0.532 Hom.: 23915

Bravo AF: 0.537

Asia WGS AF: 0.456 AC: 1581 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	5.9
DANN	Benign	0.90
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs7387468; hg19: chr8-94358098;