8-87588365-A-C

Variant names:

• chr8-87588365-A-C
• rs10504836
• ENST00000521593.5:c.340-21444A>C

Variant summary

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

The ENST00000521593.5(CNBD1):​c.340-21444A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,920 control chromosomes in the GnomAD database, including 3,599 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 0.20 (3599 hom., cov: 31)
• Consequence: CNBD1 ENST00000521593.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 3 publications found

Genes affected

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

ENSG00000253500 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521593.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNBD1	ENST00000521593.5	TSL:3	c.340-21444A>C		intron	N/A	ENSP00000427742.1
	ENSG00000253500	ENST00000440763.6	TSL:5	n.206-45876T>G		intron	N/A
	ENSG00000253500	ENST00000517711.5	TSL:3	n.233-21384T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31103 AN: 151802 Hom.: 3596 Cov.: 31

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.205 AC: 31126 AN: 151920 Hom.: 3599 Cov.: 31 AF XY: 0.202 AC XY: 15001 AN XY: 74262

African (AFR) AF: 0.0945 AC: 3921 AN: 41478

American (AMR) AF: 0.197 AC: 2997 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1211 AN: 3470

East Asian (EAS) AF: 0.167 AC: 859 AN: 5152

South Asian (SAS) AF: 0.239 AC: 1146 AN: 4800

European-Finnish (FIN) AF: 0.215 AC: 2270 AN: 10566

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17830 AN: 67910

Other (OTH) AF: 0.223 AC: 468 AN: 2102

Alfa AF: 0.248 Hom.: 15910

Bravo AF: 0.197

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10504836; hg19: chr8-88600593;