rs7821394

Variant names:

• chr8-93343791-G-A
• rs7821394
• ENST00000520096.5:n.387+2902C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-93343791-G-A
• chr8-93343791-G-T

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIBAR1-DT	ENST00000520096.5	n.387+2902C>T		intron_variant	Intron 3 of 5	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;