NM_001370523.4:c.140A>G

Variant names:

• chr16-69952050-A-G
• rs1411603419
• NM_001370523.4:c.140A>G

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_001370523.4(CLEC18A):​c.140A>G​(p.Glu47Gly) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000034 (0 hom., cov: 11)
  • Exomes 𝑓: 0.000022 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CLEC18A NM_001370523.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.83
• Publications: 0 publications found

Genes affected

CLEC18A (HGNC:30388): (C-type lectin domain family 18 member A) This is one of three closely related paralogous genes on chromosome 16 encoding secreted proteins containing C-type lectin domains. These domains bind to carbohydrates in the presence of calcium, and may be involved in cell adhesion, immune response and apoptosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2012]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.39036584).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370523.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC18A	NM_001370523.4	MANE Select	c.140A>G	p.Glu47Gly	missense	Exon 2 of 12	NP_001357452.1	A5D8T8-1
	CLEC18A	NM_001136214.4		c.140A>G	p.Glu47Gly	missense	Exon 3 of 13	NP_001129686.1	A5D8T8-1
	CLEC18A	NM_001271197.3		c.140A>G	p.Glu47Gly	missense	Exon 3 of 13	NP_001258126.1	A5D8T8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC18A	ENST00000288040.11	TSL:1 MANE Select	c.140A>G	p.Glu47Gly	missense	Exon 2 of 12	ENSP00000288040.6	A5D8T8-1
	CLEC18A	ENST00000393701.6	TSL:1	c.140A>G	p.Glu47Gly	missense	Exon 3 of 13	ENSP00000377304.2	A5D8T8-1
	CLEC18A	ENST00000568461.5	TSL:1	c.140A>G	p.Glu47Gly	missense	Exon 3 of 13	ENSP00000454685.1	A5D8T8-1

Frequencies

GnomAD3 genomes AF: 0.0000340 AC: 3 AN: 88294 Hom.: 0 Cov.: 11

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000680

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00 AC: 0 AN: 17348 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000217 AC: 11 AN: 507316 Hom.: 0 Cov.: 6 AF XY: 0.0000191 AC XY: 5 AN XY: 261750

African (AFR) AF: 0.00 AC: 0 AN: 12976

American (AMR) AF: 0.00 AC: 0 AN: 17140

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13190

East Asian (EAS) AF: 0.00 AC: 0 AN: 26464

South Asian (SAS) AF: 0.00 AC: 0 AN: 44938

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2036

European-Non Finnish (NFE) AF: 0.0000339 AC: 11 AN: 324358

Other (OTH) AF: 0.00 AC: 0 AN: 26632

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000340 AC: 3 AN: 88294 Hom.: 0 Cov.: 11 AF XY: 0.0000249 AC XY: 1 AN XY: 40128

African (AFR) AF: 0.00 AC: 0 AN: 23078

American (AMR) AF: 0.00 AC: 0 AN: 7976

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2382

East Asian (EAS) AF: 0.00 AC: 0 AN: 2468

South Asian (SAS) AF: 0.00 AC: 0 AN: 2338

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3926

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 258

European-Non Finnish (NFE) AF: 0.0000680 AC: 3 AN: 44112

Other (OTH) AF: 0.00 AC: 0 AN: 1212

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.097	T
BayesDel_noAF	Benign	-0.38
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Benign	0.075	T
Eigen	Benign	0.10
Eigen_PC	Benign	0.0070
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.81	T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.39	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.3	M
PhyloP100		4.8
PrimateAI	Uncertain	0.71	T
PROVEAN	Pathogenic	-5.5	D
REVEL	Benign	0.18
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0050	D
Polyphen		1.0	D
Vest4		0.38
MutPred		0.44		Gain of MoRF binding (P = 0.023)
MVP		0.43
MPC		3.4
ClinPred		0.99	D
GERP RS		2.5
PromoterAI		0.10	Neutral
Varity_R		0.58
gMVP		0.56

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

Other links and lift over

dbSNP: rs1411603419; hg19: chr16-69985953;