12-1631005-C-A

Variant names:

• chr12-1631005-C-A
• rs10773971
• ENST00000543071.5:c.-350C>A

Variant summary

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

The ENST00000397196.7(WNT5B):​c.-57-293C>A variant causes a intron 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WNT5B ENST00000397196.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 publications found

Genes affected

WNT5B (HGNC:16265): (Wnt family member 5B) 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 94% and 80% amino acid identity to the mouse Wnt5b protein and the human WNT5A protein, respectively. Alternative splicing of this gene generates 2 transcript variants. [provided by RefSeq, Jul 2008]

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000397196.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT5B	NM_032642.3	MANE Select	c.-57-293C>A		intron	N/A	NP_116031.1
	WNT5B	NM_030775.2		c.-57-293C>A		intron	N/A	NP_110402.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT5B	ENST00000543071.5	TSL:1	c.-350C>A		5_prime_UTR	Exon 1 of 4	ENSP00000442348.1
	WNT5B	ENST00000397196.7	TSL:1 MANE Select	c.-57-293C>A		intron	N/A	ENSP00000380379.2
	WNT5B	ENST00000310594.7	TSL:1	c.-57-293C>A		intron	N/A	ENSP00000308887.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 28458 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 14614

African (AFR) AF: 0.00 AC: 0 AN: 1094

American (AMR) AF: 0.00 AC: 0 AN: 2220

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 988

East Asian (EAS) AF: 0.00 AC: 0 AN: 2102

South Asian (SAS) AF: 0.00 AC: 0 AN: 2032

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 852

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 152

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 17384

Other (OTH) AF: 0.00 AC: 0 AN: 1634

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.21
DANN	Benign	0.56
PhyloP100		-1.1
PromoterAI		0.035	Neutral

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: rs10773971; hg19: chr12-1740171;