19-14610447-T-C

Position:

• chr19-14610447-T-C

Variant summary

Our verdict is Benign. Variant got -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

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:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC17A	NM_001204118.2	c.*251T>C		3_prime_UTR_variant	14/14	ENST00000417570.6	NP_001191047.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC17A	ENST00000417570.6	c.*251T>C		3_prime_UTR_variant	14/14	1	NM_001204118.2	ENSP00000393719	P1
CLEC17A	ENST00000547437.5	c.*357T>C		3_prime_UTR_variant	13/13	2		ENSP00000450065
CLEC17A	ENST00000339847.9			downstream_gene_variant		1		ENSP00000341620
CLEC17A	ENST00000551730.1			downstream_gene_variant		1		ENSP00000447424

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

Gnomad4 AFR exome AF: 0.0490

Gnomad4 AMR exome AF: 0.325

Gnomad4 ASJ exome AF: 0.188

Gnomad4 EAS exome AF: 0.476

Gnomad4 SAS exome AF: 0.390

Gnomad4 FIN exome AF: 0.342

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.247

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

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.208

Alfa AF: 0.235 Hom.: 5869

Bravo AF: 0.193

Asia WGS AF: 0.394 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11085900; hg19: chr19-14721259;