rs4835761

Positions:

• chr5-138082180-G-A

Variant summary

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

The XM_017009826.2(WNT8A):​c.-220-2070G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,054 control chromosomes in the GnomAD database, including 15,207 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 0.44 (15207 hom., cov: 32)
• Consequence: WNT8A XM_017009826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

WNT8A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT8A	XM_017009826.2	c.-220-2070G>A		intron_variant			XP_016865315.1
WNT8A	XM_047417692.1	c.-220-2070G>A		intron_variant			XP_047273648.1
WNT8A	XM_047417693.1	c.-220-2070G>A		intron_variant			XP_047273649.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66587 AN: 151936 Hom.: 15206 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.438 AC: 66614 AN: 152054 Hom.: 15207 Cov.: 32 AF XY: 0.442 AC XY: 32837 AN XY: 74308

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.472

Alfa AF: 0.467 Hom.: 5197

Bravo AF: 0.432

Asia WGS AF: 0.560 AC: 1952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4835761; hg19: chr5-137417869; COSMIC: COSV64230945;