ENST00000501400.1:n.949-39226A>C

Variant names:

• chr8-93603344-T-G
• rs4358777
• ENST00000501400.1:n.949-39226A>C

Variant summary

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

The ENST00000501400.1(CIBAR1-DT):​n.949-39226A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,038 control chromosomes in the GnomAD database, including 47,253 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 0.78 (47253 hom., cov: 31)
• Consequence: CIBAR1-DT ENST00000501400.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 0 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIBAR1-DT	NR_033858.1	n.949-39226A>C		intron_variant	Intron 5 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIBAR1-DT	ENST00000501400.1	n.949-39226A>C		intron_variant	Intron 5 of 10	1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118909 AN: 151920 Hom.: 47207 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.783 AC: 119015 AN: 152038 Hom.: 47253 Cov.: 31 AF XY: 0.779 AC XY: 57893 AN XY: 74318

African (AFR) AF: 0.874 AC: 36241 AN: 41484

American (AMR) AF: 0.608 AC: 9267 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2389 AN: 3462

East Asian (EAS) AF: 0.522 AC: 2688 AN: 5150

South Asian (SAS) AF: 0.807 AC: 3892 AN: 4822

European-Finnish (FIN) AF: 0.766 AC: 8098 AN: 10578

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53996 AN: 67976

Other (OTH) AF: 0.753 AC: 1588 AN: 2108

Alfa AF: 0.729 Hom.: 4133

Bravo AF: 0.765

Asia WGS AF: 0.702 AC: 2445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs4358777; hg19: chr8-94615572;