rs10504830

Positions:

• chr8-87366977-A-G

Variant summary

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

The NM_173538.3(CNBD1):​c.1303+13191A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,932 control chromosomes in the GnomAD database, including 2,972 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 (2972 hom., cov: 32)
• Consequence: CNBD1 NM_173538.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNBD1	NM_173538.3	c.1303+13191A>G		intron_variant		ENST00000518476.6	NP_775809.1
CNBD1	XM_017013149.2	c.1303+13191A>G		intron_variant			XP_016868638.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNBD1	ENST00000518476.6	c.1303+13191A>G		intron_variant		1	NM_173538.3	ENSP00000430073
CNBD1	ENST00000521593.5	c.213+13191A>G		intron_variant		3		ENSP00000427742
CNBD1	ENST00000523299.6	c.1303+13191A>G		intron_variant		3		ENSP00000430986	P1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25347 AN: 151816 Hom.: 2963 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0583

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0979

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.167 AC: 25390 AN: 151932 Hom.: 2972 Cov.: 32 AF XY: 0.167 AC XY: 12384 AN XY: 74244

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0583

Gnomad4 EAS AF: 0.0632

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0980

Gnomad4 OTH AF: 0.132

Alfa AF: 0.100 Hom.: 1613

Bravo AF: 0.173

Asia WGS AF: 0.108 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504830; hg19: chr8-88379205;