rs2336865

Variant names:

• chr8-86951252-C-T
• rs2336865
• NM_173538.3:c.431+11498C>T

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+11498C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,718 control chromosomes in the GnomAD database, including 29,222 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 0.62 (29222 hom., cov: 30)
• Consequence: CNBD1 NM_173538.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.652 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+11498C>T		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+11498C>T		intron	N/A	ENSP00000430073.1
	CNBD1	ENST00000523299.6	TSL:3	c.431+11498C>T		intron	N/A	ENSP00000430986.2

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93738 AN: 151600 Hom.: 29200 Cov.: 30

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.618 AC: 93808 AN: 151718 Hom.: 29222 Cov.: 30 AF XY: 0.620 AC XY: 45981 AN XY: 74108

African (AFR) AF: 0.568 AC: 23472 AN: 41336

American (AMR) AF: 0.662 AC: 10104 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2141 AN: 3464

East Asian (EAS) AF: 0.608 AC: 3124 AN: 5142

South Asian (SAS) AF: 0.656 AC: 3153 AN: 4808

European-Finnish (FIN) AF: 0.674 AC: 7086 AN: 10510

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.630 AC: 42774 AN: 67902

Other (OTH) AF: 0.604 AC: 1270 AN: 2102

Alfa AF: 0.627 Hom.: 14616

Bravo AF: 0.614

Asia WGS AF: 0.658 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.57
PhyloP100		0.43
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: rs2336865; hg19: chr8-87963480;