chr8-87462146-G-C

Position:

• chr8-87462146-G-C

Variant summary

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

The ENST00000523299.6(CNBD1):​c.1372-9102G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,940 control chromosomes in the GnomAD database, including 11,641 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 0.38 (11641 hom., cov: 31)
• Consequence: CNBD1 ENST00000523299.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.87462146G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNBD1	ENST00000523299.6	c.1372-9102G>C		intron_variant		3		ENSP00000430986.2
CNBD1	ENST00000521593.5	c.280-9102G>C		intron_variant		3		ENSP00000427742.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58147 AN: 151824 Hom.: 11642 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.383 AC: 58153 AN: 151940 Hom.: 11641 Cov.: 31 AF XY: 0.382 AC XY: 28394 AN XY: 74244

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.388

Alfa AF: 0.397 Hom.: 1539

Bravo AF: 0.384

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs411178; hg19: chr8-88474374;