8-93343791-G-A

Position:

• chr8-93343791-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520096.5(CIBAR1-DT):​n.387+2902C>T 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 0.535 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 ENST00000520096.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CIBAR1-DT	ENST00000520096.5	n.387+2902C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.540

Alfa AF: 0.537 Hom.: 10917

Bravo AF: 0.536

Asia WGS AF: 0.456 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7821394; hg19: chr8-94356019;