8-87040169-T-C

Position:

• chr8-87040169-T-C

Variant summary

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

The NM_173538.3(CNBD1):​c.431+100415T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.864 in 152,194 control chromosomes in the GnomAD database, including 57,269 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 0.86 (57269 hom., cov: 32)
• Consequence: CNBD1 NM_173538.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNBD1	NM_173538.3	c.431+100415T>C		intron_variant		ENST00000518476.6	NP_775809.1
CNBD1	XM_017013149.2	c.431+100415T>C		intron_variant			XP_016868638.1
CNBD1	XM_024447082.2	c.431+100415T>C		intron_variant			XP_024302850.1
CNBD1	XM_047421411.1	c.266+100415T>C		intron_variant			XP_047277367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNBD1	ENST00000518476.6	c.431+100415T>C		intron_variant		1	NM_173538.3	ENSP00000430073.1
CNBD1	ENST00000523299.6	c.431+100415T>C		intron_variant		3		ENSP00000430986.2

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131367 AN: 152076 Hom.: 57207 Cov.: 32

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.864 AC: 131490 AN: 152194 Hom.: 57269 Cov.: 32 AF XY: 0.858 AC XY: 63816 AN XY: 74400

Gnomad4 AFR AF: 0.968

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.860

Alfa AF: 0.843 Hom.: 70082

Bravo AF: 0.870

Asia WGS AF: 0.717 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.53

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: rs2943177; hg19: chr8-88052397;