rs1880473

Variant names:

• chr8-86997878-C-A
• rs1880473
• NM_173538.3:c.431+58124C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.99).
• 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 rank	MANE	Protein	UniProt
CNBD1	NM_173538.3	c.431+58124C>A		intron_variant	Intron 4 of 10	ENST00000518476.6	NP_775809.1
CNBD1	XM_017013149.2	c.431+58124C>A		intron_variant	Intron 4 of 10		XP_016868638.1
CNBD1	XM_024447082.2	c.431+58124C>A		intron_variant	Intron 4 of 6		XP_024302850.1
CNBD1	XM_047421411.1	c.266+58124C>A		intron_variant	Intron 3 of 6		XP_047277367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNBD1	ENST00000518476.6	c.431+58124C>A		intron_variant	Intron 4 of 10	1	NM_173538.3	ENSP00000430073.1
CNBD1	ENST00000523299.6	c.431+58124C>A		intron_variant	Intron 4 of 12	3		ENSP00000430986.2

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

African (AFR) AF: 0.184 AC: 7640 AN: 41456

American (AMR) AF: 0.109 AC: 1670 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1414 AN: 5152

South Asian (SAS) AF: 0.239 AC: 1149 AN: 4810

European-Finnish (FIN) AF: 0.202 AC: 2133 AN: 10572

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10450 AN: 67968

Other (OTH) AF: 0.153 AC: 321 AN: 2102

Alfa AF: 0.159 Hom.: 8516

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
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1880473; hg19: chr8-88010106;