rs7254215

Positions:

• chr19-14602681-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001204118.2(CLEC17A):​c.894+2499G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,082 control chromosomes in the GnomAD database, including 53,401 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 0.83 (53401 hom., cov: 31)
• Consequence: CLEC17A NM_001204118.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC17A	NM_001204118.2	c.894+2499G>A		intron_variant		ENST00000417570.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC17A	ENST00000417570.6	c.894+2499G>A		intron_variant		1	NM_001204118.2	P1
CLEC17A	ENST00000339847.9	c.742+2869G>A		intron_variant, NMD_transcript_variant		1
CLEC17A	ENST00000551730.1	c.*273+2499G>A		intron_variant, NMD_transcript_variant		1
CLEC17A	ENST00000547437.5	c.894+2499G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126451 AN: 151964 Hom.: 53349 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.828

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.832 AC: 126563 AN: 152082 Hom.: 53401 Cov.: 31 AF XY: 0.825 AC XY: 61314 AN XY: 74324

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.823

Alfa AF: 0.819 Hom.: 27448

Bravo AF: 0.830

Asia WGS AF: 0.626 AC: 2177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.25

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: rs7254215; hg19: chr19-14713493;