rs1036066

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024911.7(WLS):​c.107-295T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,136 control chromosomes in the GnomAD database, including 8,710 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 0.33 ( 8710 hom., cov: 32)

Consequence

WLS
NM_024911.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.987
Variant links:
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)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
WLSNM_024911.7 linkuse as main transcriptc.107-295T>G intron_variant ENST00000262348.9
GNG12-AS1NR_040077.1 linkuse as main transcriptn.1229-7447A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WLSENST00000262348.9 linkuse as main transcriptc.107-295T>G intron_variant 1 NM_024911.7 P1Q5T9L3-1
GNG12-AS1ENST00000420587.5 linkuse as main transcriptn.1214-7447A>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.335
AC:
50911
AN:
152018
Hom.:
8706
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.389
Gnomad AMI
AF:
0.410
Gnomad AMR
AF:
0.308
Gnomad ASJ
AF:
0.325
Gnomad EAS
AF:
0.369
Gnomad SAS
AF:
0.327
Gnomad FIN
AF:
0.212
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.324
Gnomad OTH
AF:
0.345
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.335
AC:
50938
AN:
152136
Hom.:
8710
Cov.:
32
AF XY:
0.332
AC XY:
24683
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.388
Gnomad4 AMR
AF:
0.308
Gnomad4 ASJ
AF:
0.325
Gnomad4 EAS
AF:
0.368
Gnomad4 SAS
AF:
0.328
Gnomad4 FIN
AF:
0.212
Gnomad4 NFE
AF:
0.324
Gnomad4 OTH
AF:
0.342
Alfa
AF:
0.322
Hom.:
2121
Bravo
AF:
0.344
Asia WGS
AF:
0.349
AC:
1216
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.32
DANN
Benign
0.60

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1036066; hg19: chr1-68660205; API