chr1-228059650-T-C

Variant names:

• chr1-228059650-T-C
• rs752107
• NM_033131.4:c.*185T>C

Variant summary

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

The NM_033131.4(WNT3A):​c.*185T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 1,366,316 control chromosomes in the GnomAD database, including 315,672 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 0.72 (39765 hom., cov: 33)
  • Exomes 𝑓: 0.67 (275907 hom.)
• Consequence: WNT3A NM_033131.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 31 publications found

Genes affected

WNT3A (HGNC:15983): (Wnt family member 3A) 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 96% amino acid identity to mouse Wnt3A protein, and 84% to human WNT3 protein, another WNT gene product. This gene is clustered with WNT14 gene, another family member, in chromosome 1q42 region. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033131.4. 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
	WNT3A	NM_033131.4	MANE Select	c.*185T>C		3_prime_UTR	Exon 4 of 4	NP_149122.1	P56704-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WNT3A	ENST00000284523.2	TSL:1 MANE Select	c.*185T>C		3_prime_UTR	Exon 4 of 4	ENSP00000284523.1	P56704-1
	WNT3A	ENST00000948304.1		c.*185T>C		3_prime_UTR	Exon 4 of 4	ENSP00000618363.1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109620 AN: 151912 Hom.: 39735 Cov.: 33

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.712

GnomAD4 exome AF: 0.673 AC: 817005 AN: 1214286 Hom.: 275907 Cov.: 52 AF XY: 0.675 AC XY: 393672 AN XY: 583534

African (AFR) AF: 0.804 AC: 19177 AN: 23838

American (AMR) AF: 0.709 AC: 8640 AN: 12178

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 11332 AN: 17306

East Asian (EAS) AF: 0.776 AC: 22577 AN: 29090

South Asian (SAS) AF: 0.768 AC: 37852 AN: 49256

European-Finnish (FIN) AF: 0.738 AC: 21389 AN: 28968

Middle Eastern (MID) AF: 0.715 AC: 2439 AN: 3410

European-Non Finnish (NFE) AF: 0.659 AC: 658679 AN: 999888

Other (OTH) AF: 0.694 AC: 34920 AN: 50352

GnomAD4 genome AF: 0.722 AC: 109704 AN: 152030 Hom.: 39765 Cov.: 33 AF XY: 0.727 AC XY: 54049 AN XY: 74320

African (AFR) AF: 0.793 AC: 32906 AN: 41494

American (AMR) AF: 0.707 AC: 10811 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2272 AN: 3468

East Asian (EAS) AF: 0.786 AC: 4031 AN: 5126

South Asian (SAS) AF: 0.781 AC: 3764 AN: 4820

European-Finnish (FIN) AF: 0.752 AC: 7977 AN: 10606

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.671 AC: 45578 AN: 67924

Other (OTH) AF: 0.713 AC: 1498 AN: 2102

Alfa AF: 0.687 Hom.: 32089

Bravo AF: 0.721

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-1.7
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: rs752107; hg19: chr1-228247351;