1-68166800-C-T

Variant summary

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

The NM_024911.7(WLS):c.380-7553G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,988 control chromosomes in the GnomAD database, including 22,891 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 0.54 (22891 hom., cov: 32)
• Consequence: WLS NM_024911.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671

Genes affected

WLS (HGNC:30238): (Wnt ligand secretion mediator) Enables Wnt-protein binding activity and identical protein binding activity. Involved in positive regulation of cell communication and protein transport. Located in several cellular components, including Golgi apparatus; early endosome; and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

GNG12-AS1 (HGNC:43938): (GNG12, DIRAS3 and WLS antisense RNA 1)

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 = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WLS	NM_024911.7	c.380-7553G>A		intron_variant		ENST00000262348.9
GNG12-AS1	NR_040077.1	n.1228+28350C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WLS	ENST00000262348.9	c.380-7553G>A		intron_variant		1	NM_024911.7	P1
GNG12-AS1	ENST00000420587.5	n.1213+28350C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82438 AN: 151870 Hom.: 22879 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.543 AC: 82491 AN: 151988 Hom.: 22891 Cov.: 32 AF XY: 0.549 AC XY: 40781 AN XY: 74298

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.545

Alfa AF: 0.547 Hom.: 13165

Bravo AF: 0.533

Asia WGS AF: 0.697 AC: 2424 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	0.72
Dann	Benign	0.84

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

Publications

LitVar

Other links and lift over

dbSNP: rs2566758; hg19: chr1-68632483;