8-87518633-C-T

Variant names:

• chr8-87518633-C-T
• rs436753
• ENST00000521593.5:c.339+47326C>T

Variant summary

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

The ENST00000521593.5(CNBD1):​c.339+47326C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,798 control chromosomes in the GnomAD database, including 2,334 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 0.16 (2334 hom., cov: 32)
• Consequence: CNBD1 ENST00000521593.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 2 publications found

Genes affected

CNBD1 (HGNC:26663): (cyclic nucleotide binding domain containing 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.312 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
CNBD1	ENST00000521593.5	c.339+47326C>T		intron_variant	Intron 4 of 7	3		ENSP00000427742.1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23899 AN: 151680 Hom.: 2332 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0864

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.158 AC: 23915 AN: 151798 Hom.: 2334 Cov.: 32 AF XY: 0.159 AC XY: 11777 AN XY: 74170

African (AFR) AF: 0.131 AC: 5406 AN: 41424

American (AMR) AF: 0.320 AC: 4862 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1533 AN: 5158

South Asian (SAS) AF: 0.142 AC: 685 AN: 4814

European-Finnish (FIN) AF: 0.0864 AC: 912 AN: 10554

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9594 AN: 67866

Other (OTH) AF: 0.153 AC: 322 AN: 2110

Alfa AF: 0.154 Hom.: 3034

Bravo AF: 0.175

Asia WGS AF: 0.219 AC: 756 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs436753; hg19: chr8-88530861;