chr16-78030836-C-G

Position:

• chr16-78030836-C-G

Variant summary

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

The ENST00000299642.10(CLEC3A):​c.589C>G​(p.Gln197Glu) 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. 13/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q197K) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: CLEC3A ENST00000299642.10 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.14

Genes affected

CLEC3A (HGNC:2052): (C-type lectin domain family 3 member A) Predicted to enable carbohydrate binding activity. Predicted to be involved in ossification. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

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=0.072229505).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC3A	NM_005752.6	c.589C>G	p.Gln197Glu	missense_variant	3/3	ENST00000299642.10	NP_005743.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC3A	ENST00000299642.10	c.589C>G	p.Gln197Glu	missense_variant	3/3	1	NM_005752.6	ENSP00000299642	P1
	ENST00000563114.1	n.42-15707G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.072
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.6
DANN	Benign	0.92
Eigen	Benign	-0.76
Eigen_PC	Benign	-0.63
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.41	T
M_CAP	Benign	0.0054	T
MetaRNN	Benign	0.072	T
MetaSVM	Benign	-1.0	T
MutationTaster	Benign	1.0	P;P
PrimateAI	Benign	0.33	T
REVEL	Benign	0.063
Sift4G	Pathogenic	0.0	D
Vest4		0.13
MVP		0.076
MPC		0.0015
ClinPred		0.13	T
GERP RS		3.9

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: rs2072663; hg19: chr16-78064733;