rs7207916

Positions:

• chr17-46801984-G-A

Variant summary

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

The ENST00000225512.6(WNT3):​c.80+16534C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,126 control chromosomes in the GnomAD database, including 8,068 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 0.29 (8068 hom., cov: 33)
• Consequence: WNT3 ENST00000225512.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532

Genes affected

WNT3 (HGNC:12782): (Wnt family member 3) 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 encodes a protein which shows 98% amino acid identity to mouse Wnt3 protein, and 84% to human WNT3A protein, another WNT gene product. The mouse studies show the requirement of Wnt3 in primary axis formation in the mouse. Studies of the gene expression suggest that this gene may play a key role in some cases of human breast, rectal, lung, and gastric cancer through activation of the WNT-beta-catenin-TCF signaling pathway. This gene is clustered with WNT15, another family member, in the chromosome 17q21 region. [provided by RefSeq, Jul 2008]

LRRC37A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT3	NM_030753.5	c.80+16534C>T		intron_variant		ENST00000225512.6	NP_110380.1
LRRC37A2	XM_024450773.2	c.4810-247072G>A		intron_variant			XP_024306541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT3	ENST00000225512.6	c.80+16534C>T		intron_variant		1	NM_030753.5	ENSP00000225512	P1
WNT3	ENST00000706495.1	c.-115-28075C>T		intron_variant				ENSP00000516418
WNT3	ENST00000573788.5	n.491+19124C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44789 AN: 152008 Hom.: 8065 Cov.: 33

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.294 AC: 44792 AN: 152126 Hom.: 8068 Cov.: 33 AF XY: 0.293 AC XY: 21787 AN XY: 74368

Gnomad4 AFR AF: 0.0746

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.311

Alfa AF: 0.372 Hom.: 6104

Bravo AF: 0.281

Asia WGS AF: 0.254 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.64

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: rs7207916; hg19: chr17-44879350;