rs1880473

chr8-86997878-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173538.3(CNBD1):c.431+58124C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,996 control chromosomes in the GnomAD database, including 2,256 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 0.17 (2256 hom., cov: 31)
• Consequence: CNBD1 NM_173538.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNBD1	NM_173538.3	c.431+58124C>A		intron_variant		ENST00000518476.6
CNBD1	XM_017013149.2	c.431+58124C>A		intron_variant
CNBD1	XM_024447082.2	c.431+58124C>A		intron_variant
CNBD1	XM_047421411.1	c.266+58124C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNBD1	ENST00000518476.6	c.431+58124C>A		intron_variant		1	NM_173538.3
CNBD1	ENST00000523299.6	c.431+58124C>A		intron_variant		3		P1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25558 AN: 151880 Hom.: 2255 Cov.: 31

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.168 AC: 25579 AN: 151996 Hom.: 2256 Cov.: 31 AF XY: 0.172 AC XY: 12754 AN XY: 74314

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.153

Alfa AF: 0.157 Hom.: 3986

Bravo AF: 0.162

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.69
Dann	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880473; hg19: chr8-88010106;