rs3803884

Variant names:

• chr17-50841678-C-A
• rs3803884
• NM_175575.6:c.*659C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-50841678-C-A
• chr17-50841678-C-T

Variant summary

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

The NM_175575.6(WFIKKN2):​c.*659C>A 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: 30)
• Consequence: WFIKKN2 NM_175575.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 7 publications found

Genes affected

WFIKKN2 (HGNC:30916): (WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2) The WFIKKN1 protein contains a WAP domain, follistatin domain, immunoglobulin domain, two tandem Kunitz domains, and an NTR domain. This gene encodes a WFIKKN1-related protein which has the same domain organization as the WFIKKN1 protein. The WAP-type, follistatin type, Kunitz-type, and NTR-type protease inhibitory domains may control the action of multiple types of proteases. [provided by RefSeq, Jul 2008]

ENSG00000261976 (HGNC:):

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=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WFIKKN2	NM_175575.6	c.*659C>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000311378.5	NP_783165.1
WFIKKN2	NM_001330341.2	c.*659C>A		3_prime_UTR_variant	Exon 2 of 2		NP_001317270.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WFIKKN2	ENST00000311378.5	c.*659C>A		3_prime_UTR_variant	Exon 2 of 2	1	NM_175575.6	ENSP00000311184.4
ENSG00000261976	ENST00000759459.1	n.323G>T		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000261976	ENST00000759460.1	n.282G>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000261976	ENST00000572491.2	n.-52G>T		upstream_gene_variant		5

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.47
PhyloP100		-0.90

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: rs3803884; hg19: chr17-48919039;