rs10504836

Positions:

• chr8-87588365-A-C
• chr8-87588365-A-G
• chr8-87588365-A-T

Variant summary

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

The ENST00000440763.6(ENSG00000253500):​n.206-45876T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,920 control chromosomes in the GnomAD database, including 3,599 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 0.20 (3599 hom., cov: 31)
• Consequence: ENST00000440763.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

(HGNC:):

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000440763.6	n.206-45876T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31103 AN: 151802 Hom.: 3596 Cov.: 31

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.205 AC: 31126 AN: 151920 Hom.: 3599 Cov.: 31 AF XY: 0.202 AC XY: 15001 AN XY: 74262

Gnomad4 AFR AF: 0.0945

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.223

Alfa AF: 0.259 Hom.: 10894

Bravo AF: 0.197

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504836; hg19: chr8-88600593;