rs411178

Variant names:

• chr8-87462146-G-C
• rs411178
• ENST00000523299.6:c.1372-9102G>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)

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNBD1	ENST00000523299.6	c.1372-9102G>C		intron_variant	Intron 11 of 12	3		ENSP00000430986.2
CNBD1	ENST00000521593.5	c.280-9102G>C		intron_variant	Intron 3 of 7	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;