chr16-84304628-T-C

Variant names:

• chr16-84304628-T-C
• rs16963349
• NM_021197.4:c.145-8333T>C

Variant summary

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

The NM_021197.4(WFDC1):​c.145-8333T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0708 in 152,250 control chromosomes in the GnomAD database, including 1,197 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 0.071 (1197 hom., cov: 33)
• Consequence: WFDC1 NM_021197.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 5 publications found

Genes affected

WFDC1 (HGNC:15466): (WAP four-disulfide core domain 1) This gene encodes a member of the WAP-type four disulfide core domain family. The WAP-type four-disulfide core domain contains eight cysteines forming four disulfide bonds at the core of the protein, and functions as a protease inhibitor in many family members. This gene is mapped to chromosome 16q24, an area of frequent loss of heterozygosity in cancers, including prostate, breast and hepatocellular cancers and Wilms' tumor. This gene is downregulated in many cancer types and may be involved in the inhibition of cell proliferation. The encoded protein may also play a role in the susceptibility of certain CD4 memory T cells to human immunodeficiency virus infection. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021197.4. 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
	WFDC1	NM_021197.4	MANE Select	c.145-8333T>C		intron	N/A	NP_067020.2
	WFDC1	NM_001282466.2		c.145-8333T>C		intron	N/A	NP_001269395.1
	WFDC1	NM_001282467.2		c.145-8333T>C		intron	N/A	NP_001269396.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WFDC1	ENST00000219454.10	TSL:1 MANE Select	c.145-8333T>C		intron	N/A	ENSP00000219454.5
	WFDC1	ENST00000568638.1	TSL:2	c.145-8333T>C		intron	N/A	ENSP00000456920.1
	WFDC1	ENST00000943489.1		c.145-8333T>C		intron	N/A	ENSP00000613548.1

Frequencies

GnomAD3 genomes AF: 0.0706 AC: 10739 AN: 152132 Hom.: 1194 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00125

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0708 AC: 10779 AN: 152250 Hom.: 1197 Cov.: 33 AF XY: 0.0699 AC XY: 5203 AN XY: 74448

African (AFR) AF: 0.237 AC: 9827 AN: 41508

American (AMR) AF: 0.0271 AC: 415 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00260 AC: 9 AN: 3464

East Asian (EAS) AF: 0.0127 AC: 66 AN: 5188

South Asian (SAS) AF: 0.0491 AC: 237 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00125 AC: 85 AN: 68028

Other (OTH) AF: 0.0577 AC: 122 AN: 2114

Alfa AF: 0.0325 Hom.: 219

Bravo AF: 0.0783

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.058
DANN	Benign	0.66
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs16963349; hg19: chr16-84338234;