rs10504836

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-87588365-A-C
• chr8-87588365-A-G
• chr8-87588365-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ENSG00000253500 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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.340-21444A>C		intron_variant	Intron 4 of 7	3		ENSP00000427742.1
ENSG00000253500	ENST00000440763.6	n.206-45876T>G		intron_variant	Intron 3 of 3	5
ENSG00000253500	ENST00000517711.5	n.233-21384T>G		intron_variant	Intron 3 of 3	3

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

Gnomad4 AFR AF: 0.0945

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.223

Alfa AF: 0.259 Hom.: 10894

Bravo AF: 0.197

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504836; hg19: chr8-88600593;