Variant chr7-121329771-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_057168.2(WNT16):c.300C>A(p.Thr100Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00702 in 1,608,816 control chromosomes in the GnomAD database, including 110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.013 ( 27 hom., cov: 34)

Exomes 𝑓: 0.0064 ( 83 hom. )

Consequence

WNT16
NM_057168.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.818

Variant links:

Genes affected

WNT16 (HGNC:16267): (Wnt family member 16) The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It contains two transcript variants diverging at the 5' termini. These two variants are proposed to be the products of separate promoters and not to be splice variants from a single promoter. They are differentially expressed in normal tissues, one of which (variant 2) is expressed at significant levels only in the pancreas, whereas another one (variant 1) is expressed more ubiquitously with highest levels in adult kidney, placenta, brain, heart, and spleen. [provided by RefSeq, Jul 2008]

WNT16 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 7-121329771-C-A is Benign according to our data. Variant chr7-121329771-C-A is described in ClinVar as [Benign]. Clinvar id is 781654.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.818 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1948/152366) while in subpopulation AFR AF= 0.023 (958/41600). AF 95% confidence interval is 0.0218. There are 27 homozygotes in gnomad4. There are 968 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 27 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT16	NM_057168.2 linkuse as main transcript	c.300C>A	p.Thr100Thr	synonymous_variant	2/4	ENST00000222462.3	NP_476509.1	Q9UBV4-1
WNT16	NM_016087.2 linkuse as main transcript	c.270C>A	p.Thr90Thr	synonymous_variant	2/4		NP_057171.2	Q9UBV4E9PH60

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT16	ENST00000222462.3 linkuse as main transcript	c.300C>A	p.Thr100Thr	synonymous_variant	2/4	1	NM_057168.2	ENSP00000222462.2		Q9UBV4-1
WNT16	ENST00000361301.6 linkuse as main transcript	c.270C>A	p.Thr90Thr	synonymous_variant	2/4	1		ENSP00000355065.2		E9PH60

Frequencies

GnomAD3 genomes

AF:

0.0128

AC:

1944

AN:

152248

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0230

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0131

Gnomad ASJ

AF:

0.0288

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.00517

Gnomad FIN

AF:

0.0120

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00663

Gnomad OTH

AF:

0.0167

GnomAD3 exomes

AF:

0.00897

AC:

2194

AN:

244660

Hom.:

AF XY:

0.00854

AC XY:

1137

AN XY:

133200

show subpopulations

Gnomad AFR exome

AF:

0.0236

Gnomad AMR exome

AF:

0.00710

Gnomad ASJ exome

AF:

0.0293

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00389

Gnomad FIN exome

AF:

0.0143

Gnomad NFE exome

AF:

0.00742

Gnomad OTH exome

AF:

0.0141

GnomAD4 exome

AF:

0.00641

AC:

9342

AN:

1456450

Hom.:

Cov.:

AF XY:

0.00645

AC XY:

4676

AN XY:

724712

show subpopulations

Gnomad4 AFR exome

AF:

0.0259

Gnomad4 AMR exome

AF:

0.00769

Gnomad4 ASJ exome

AF:

0.0283

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00383

Gnomad4 FIN exome

AF:

0.0128

Gnomad4 NFE exome

AF:

0.00507

Gnomad4 OTH exome

AF:

0.0110

GnomAD4 genome

AF:

0.0128

AC:

1948

AN:

152366

Hom.:

Cov.:

AF XY:

0.0130

AC XY:

968

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.0230

Gnomad4 AMR

AF:

0.0130

Gnomad4 ASJ

AF:

0.0288

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00539

Gnomad4 FIN

AF:

0.0120

Gnomad4 NFE

AF:

0.00663

Gnomad4 OTH

AF:

0.0165

Alfa

AF:

0.00669

Hom.:

Bravo

AF:

0.0135

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.00921

EpiControl

AF:

0.00859

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 08, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

2.1

DANN

Benign

0.61

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over