NM_173478.3:c.719T>A

Variant names:

• chr17-42806812-T-A
• NM_173478.3:c.719T>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_173478.3(CNTD1):​c.719T>A​(p.Leu240Gln) 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. 12/19 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: 32)
• Consequence: CNTD1 NM_173478.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.17

Genes affected

CNTD1 (HGNC:26847): (cyclin N-terminal domain containing 1) Predicted to be involved in reciprocal meiotic recombination. Predicted to act upstream of or within spermatogenesis. Predicted to be active in site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16998142).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTD1	NM_173478.3	c.719T>A	p.Leu240Gln	missense_variant	Exon 5 of 7	ENST00000588408.6	NP_775749.2
CNTD1	NM_001330222.2	c.470T>A	p.Leu157Gln	missense_variant	Exon 5 of 7		NP_001317151.1
CNTD1	XM_024450569.2	c.563T>A	p.Leu188Gln	missense_variant	Exon 5 of 7		XP_024306337.1
CNTD1	XM_011524311.3	c.470T>A	p.Leu157Gln	missense_variant	Exon 4 of 6		XP_011522613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTD1	ENST00000588408.6	c.719T>A	p.Leu240Gln	missense_variant	Exon 5 of 7	1	NM_173478.3	ENSP00000465204.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.085
BayesDel_addAF	Benign	-0.059	T
BayesDel_noAF	Benign	-0.32
CADD	Benign	22
DANN	Benign	0.91
DEOGEN2	Benign	0.0080	T;T;.
Eigen	Benign	0.059
Eigen_PC	Benign	0.17
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Benign	0.72	T;T;T
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.17	T;T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	1.7	L;.;.
PrimateAI	Uncertain	0.52	T
Sift4G	Benign	0.30	T;T;T
Polyphen		0.58	P;.;.
Vest4		0.32
MutPred		0.35		Gain of solvent accessibility (P = 0.0149);.;.;
MVP		0.61
MPC		0.22
ClinPred		0.59	D
GERP RS		4.0
Varity_R		0.48
gMVP		0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr17-40958830;