NM_001204118.2:c.*251T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001204118.2(CLEC17A):​c.*251T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 510,290 control chromosomes in the GnomAD database, including 19,447 homozygotes. 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: 𝑓 0.21 (4207 hom., cov: 31)
  • Exomes 𝑓: 0.27 (15240 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC17A	NM_001204118.2	MANE Select	c.*251T>C		3_prime_UTR	Exon 14 of 14	NP_001191047.1
	CLEC17A	NM_207390.4		c.*357T>C		3_prime_UTR	Exon 13 of 13	NP_997273.3
	CLEC17A	NR_109784.2		n.1528T>C		non_coding_transcript_exon	Exon 14 of 14

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31556 AN: 151830 Hom.: 4202 Cov.: 31

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.206

GnomAD4 exome AF: 0.275 AC: 98518 AN: 358342 Hom.: 15240 Cov.: 3 AF XY: 0.283 AC XY: 53400 AN XY: 188810

African (AFR) AF: 0.0490 AC: 514 AN: 10490

American (AMR) AF: 0.325 AC: 4889 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 2092 AN: 11126

East Asian (EAS) AF: 0.476 AC: 11333 AN: 23784

South Asian (SAS) AF: 0.390 AC: 15697 AN: 40262

European-Finnish (FIN) AF: 0.342 AC: 7337 AN: 21444

Middle Eastern (MID) AF: 0.265 AC: 428 AN: 1616

European-Non Finnish (NFE) AF: 0.239 AC: 51108 AN: 213840

Other (OTH) AF: 0.247 AC: 5120 AN: 20750

GnomAD4 genome AF: 0.208 AC: 31565 AN: 151948 Hom.: 4207 Cov.: 31 AF XY: 0.217 AC XY: 16139 AN XY: 74242

African (AFR) AF: 0.0494 AC: 2052 AN: 41498

American (AMR) AF: 0.296 AC: 4505 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2170 AN: 5154

South Asian (SAS) AF: 0.380 AC: 1830 AN: 4820

European-Finnish (FIN) AF: 0.337 AC: 3552 AN: 10534

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16072 AN: 67926

Other (OTH) AF: 0.208 AC: 439 AN: 2110

Alfa AF: 0.230 Hom.: 7137

Bravo AF: 0.193

Asia WGS AF: 0.394 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.86
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

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;