chr8-86994886-A-G

Variant names:

• chr8-86994886-A-G
• rs1852027
• NM_173538.3:c.431+55132A>G

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+55132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,904 control chromosomes in the GnomAD database, including 23,679 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 0.56 (23679 hom., cov: 31)
• Consequence: CNBD1 NM_173538.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173538.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNBD1	NM_173538.3	MANE Select	c.431+55132A>G		intron	N/A	NP_775809.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNBD1	ENST00000518476.6	TSL:1 MANE Select	c.431+55132A>G		intron	N/A	ENSP00000430073.1
	CNBD1	ENST00000523299.6	TSL:3	c.431+55132A>G		intron	N/A	ENSP00000430986.2

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84562 AN: 151786 Hom.: 23666 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.557 AC: 84618 AN: 151904 Hom.: 23679 Cov.: 31 AF XY: 0.561 AC XY: 41678 AN XY: 74236

African (AFR) AF: 0.500 AC: 20708 AN: 41420

American (AMR) AF: 0.589 AC: 9002 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1865 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3138 AN: 5146

South Asian (SAS) AF: 0.577 AC: 2774 AN: 4806

European-Finnish (FIN) AF: 0.586 AC: 6176 AN: 10548

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.577 AC: 39207 AN: 67940

Other (OTH) AF: 0.540 AC: 1138 AN: 2108

Alfa AF: 0.564 Hom.: 43961

Bravo AF: 0.553

Asia WGS AF: 0.564 AC: 1965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-0.089
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: rs1852027; hg19: chr8-88007114;