3-55491957-T-G

Position:

• chr3-55491957-T-G

Variant summary

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

The XM_047448853.1(WNT5A):​c.-1967A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,090 control chromosomes in the GnomAD database, including 24,114 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 0.55 (24114 hom., cov: 33)
• Consequence: WNT5A XM_047448853.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

Genes affected

WNT5A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNT5A	XM_047448853.1	c.-1967A>C		5_prime_UTR_variant	5/9
WNT5A	XM_047448854.1	c.-1967A>C		5_prime_UTR_variant	6/10
WNT5A	XM_047448855.1	c.-1967A>C		5_prime_UTR_variant	4/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83989 AN: 151972 Hom.: 24078 Cov.: 33

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.553 AC: 84082 AN: 152090 Hom.: 24114 Cov.: 33 AF XY: 0.552 AC XY: 41028 AN XY: 74352

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.537

Alfa AF: 0.452 Hom.: 2364

Bravo AF: 0.552

Asia WGS AF: 0.499 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.62
DANN	Benign	0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs524153; hg19: chr3-55525985;