19-14610447-T-G

Variant names:

• chr19-14610447-T-G
• rs11085900
• NM_001204118.2:c.*251T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001204118.2(CLEC17A):​c.*251T>G variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: CLEC17A NM_001204118.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 9 publications found

Genes affected

CLEC17A (HGNC:34520): (C-type lectin domain containing 17A) Enables fucose binding activity; identical protein binding activity; and mannose binding activity. Located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

ADGRE3 (HGNC:23647): (adhesion G protein-coupled receptor E3) This gene encodes a member of the class B seven-span transmembrane (TM7) receptor family expressed predominantly by cells of the immune system. Family members are characterized by an extended extracellular region with a variable number of N-terminal epidermal growth factor (EGF)-like domains coupled to a TM7 domain via a mucin-like spacer domain. This gene is closely linked to the gene encoding egf-like molecule containing mucin-like hormone receptor 2 on chromosome 19. This protein may play a role in myeloid-myeloid interactions during immune and inflammatory responses. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2014]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204118.2. 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
	CLEC17A	NM_001204118.2	MANE Select	c.*251T>G		3_prime_UTR	Exon 14 of 14	NP_001191047.1	Q6ZS10-1
	CLEC17A	NM_207390.4		c.*357T>G		3_prime_UTR	Exon 13 of 13	NP_997273.3	Q6ZS10-3
	CLEC17A	NR_109784.2		n.1528T>G		non_coding_transcript_exon	Exon 14 of 14

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC17A	ENST00000417570.6	TSL:1 MANE Select	c.*251T>G		3_prime_UTR	Exon 14 of 14	ENSP00000393719.2	Q6ZS10-1
	CLEC17A	ENST00000547437.5	TSL:2	c.*357T>G		3_prime_UTR	Exon 13 of 13	ENSP00000450065.1	Q6ZS10-3
	ADGRE3	ENST00000718247.1		c.1921-10185A>C		intron	N/A	ENSP00000520692.1	A0ABB0MV84

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 3

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 7137

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.85
PhyloP100		0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11085900; hg19: chr19-14721259;