chr8-87286642-T-C

Variant names:

• chr8-87286642-T-C
• NM_173538.3:c.1013T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_173538.3(CNBD1):​c.1013T>C​(p.Leu338Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CNBD1 NM_173538.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22716194).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNBD1	NM_173538.3	c.1013T>C	p.Leu338Pro	missense_variant	Exon 8 of 11	ENST00000518476.6	NP_775809.1
CNBD1	XM_017013149.2	c.1013T>C	p.Leu338Pro	missense_variant	Exon 8 of 11		XP_016868638.1
CNBD1	XM_047421411.1	c.848T>C	p.Leu283Pro	missense_variant	Exon 7 of 7		XP_047277367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNBD1	ENST00000518476.6	c.1013T>C	p.Leu338Pro	missense_variant	Exon 8 of 11	1	NM_173538.3	ENSP00000430073.1
CNBD1	ENST00000523299.6	c.1013T>C	p.Leu338Pro	missense_variant	Exon 8 of 13	3		ENSP00000430986.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.76
BayesDel_addAF	Benign	-0.021	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.16	T;.
Eigen	Benign	-0.36
Eigen_PC	Benign	-0.42
FATHMM_MKL	Benign	0.090	N
LIST_S2	Benign	0.44	T;T
M_CAP	Benign	0.0065	T
MetaRNN	Benign	0.23	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N;.
PrimateAI	Benign	0.40	T
PROVEAN	Uncertain	-3.8	D;.
REVEL	Benign	0.22
Sift	Uncertain	0.027	D;.
Sift4G	Benign	0.068	T;T
Polyphen		0.85	P;.
Vest4		0.57
MutPred		0.63		Loss of helix (P = 0.0017);.;
MVP		0.27
MPC		0.0060
ClinPred		0.35	T
GERP RS		1.8
PromoterAI		-0.020	Neutral
Varity_R		0.32
gMVP		0.36
Mutation Taster		=89/11	polymorphism

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-88298870;