12-1631005-C-G

Variant names:

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

Variant summary

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

The ENST00000543071.5(WNT5B):​c.-350C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0659 in 180,624 control chromosomes in the GnomAD database, including 734 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 0.069 (634 hom., cov: 32)
  • Exomes 𝑓: 0.047 (100 hom.)
• Consequence: WNT5B ENST00000543071.5 5_prime_UTR
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000543071.5. 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>G		intron	N/A	NP_116031.1
	WNT5B	NM_030775.2		c.-57-293C>G		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>G		5_prime_UTR	Exon 1 of 4	ENSP00000442348.1
	WNT5B	ENST00000397196.7	TSL:1 MANE Select	c.-57-293C>G		intron	N/A	ENSP00000380379.2
	WNT5B	ENST00000310594.7	TSL:1	c.-57-293C>G		intron	N/A	ENSP00000308887.3

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10536 AN: 152064 Hom.: 632 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0574

GnomAD4 exome AF: 0.0469 AC: 1334 AN: 28442 Hom.: 100 Cov.: 0 AF XY: 0.0436 AC XY: 637 AN XY: 14608

African (AFR) AF: 0.124 AC: 135 AN: 1092

American (AMR) AF: 0.0523 AC: 116 AN: 2218

Ashkenazi Jewish (ASJ) AF: 0.0152 AC: 15 AN: 988

East Asian (EAS) AF: 0.264 AC: 553 AN: 2096

South Asian (SAS) AF: 0.0630 AC: 128 AN: 2032

European-Finnish (FIN) AF: 0.0235 AC: 20 AN: 850

Middle Eastern (MID) AF: 0.0329 AC: 5 AN: 152

European-Non Finnish (NFE) AF: 0.0174 AC: 302 AN: 17380

Other (OTH) AF: 0.0367 AC: 60 AN: 1634

GnomAD4 genome AF: 0.0694 AC: 10561 AN: 152182 Hom.: 634 Cov.: 32 AF XY: 0.0706 AC XY: 5257 AN XY: 74410

African (AFR) AF: 0.148 AC: 6138 AN: 41502

American (AMR) AF: 0.0624 AC: 953 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1179 AN: 5166

South Asian (SAS) AF: 0.0692 AC: 334 AN: 4830

European-Finnish (FIN) AF: 0.0363 AC: 385 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0203 AC: 1382 AN: 68002

Other (OTH) AF: 0.0616 AC: 130 AN: 2112

Alfa AF: 0.0470 Hom.: 46

Bravo AF: 0.0743

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.22
DANN	Benign	0.31
PhyloP100		-1.1
PromoterAI		0.023	Neutral
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: rs10773971; hg19: chr12-1740171;