chr10-48913380-G-C

Variant summary

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

The NM_001394531.1(WDFY4):​c.7586+11517G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,605,578 control chromosomes in the GnomAD database, including 14,229 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 0.14 ( 1575 hom., cov: 30)
Exomes 𝑓: 0.13 ( 12654 hom. )

Consequence

WDFY4
NM_001394531.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.92
Variant links:
Genes affected
LRRC18 (HGNC:23199): (leucine rich repeat containing 18) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
WDFY4 (HGNC:29323): (WDFY family member 4) Predicted to be involved in autophagy. Predicted to act upstream of or within with a positive effect on CD8-positive, alpha-beta T cell activation. Predicted to act upstream of or within antigen processing and presentation and cellular response to virus. Predicted to be located in early endosome and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.48).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRRC18NM_001378102.1 linkuse as main transcriptc.764+12C>G intron_variant ENST00000374160.8
WDFY4NM_001394531.1 linkuse as main transcriptc.7586+11517G>C intron_variant ENST00000325239.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
WDFY4ENST00000325239.12 linkuse as main transcriptc.7586+11517G>C intron_variant 5 NM_001394531.1 P1Q6ZS81-1
LRRC18ENST00000374160.8 linkuse as main transcriptc.764+12C>G intron_variant 1 NM_001378102.1 P1Q8N456-1
ENST00000430438.1 linkuse as main transcriptn.173+19106C>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.136
AC:
20676
AN:
151658
Hom.:
1571
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.175
Gnomad AMI
AF:
0.108
Gnomad AMR
AF:
0.102
Gnomad ASJ
AF:
0.184
Gnomad EAS
AF:
0.00194
Gnomad SAS
AF:
0.162
Gnomad FIN
AF:
0.140
Gnomad MID
AF:
0.210
Gnomad NFE
AF:
0.126
Gnomad OTH
AF:
0.134
GnomAD3 exomes
AF:
0.121
AC:
29514
AN:
244604
Hom.:
2167
AF XY:
0.126
AC XY:
16672
AN XY:
132580
show subpopulations
Gnomad AFR exome
AF:
0.178
Gnomad AMR exome
AF:
0.0718
Gnomad ASJ exome
AF:
0.185
Gnomad EAS exome
AF:
0.000327
Gnomad SAS exome
AF:
0.173
Gnomad FIN exome
AF:
0.135
Gnomad NFE exome
AF:
0.124
Gnomad OTH exome
AF:
0.140
GnomAD4 exome
AF:
0.127
AC:
184362
AN:
1453802
Hom.:
12654
Cov.:
32
AF XY:
0.129
AC XY:
93219
AN XY:
723018
show subpopulations
Gnomad4 AFR exome
AF:
0.180
Gnomad4 AMR exome
AF:
0.0751
Gnomad4 ASJ exome
AF:
0.187
Gnomad4 EAS exome
AF:
0.000277
Gnomad4 SAS exome
AF:
0.171
Gnomad4 FIN exome
AF:
0.133
Gnomad4 NFE exome
AF:
0.126
Gnomad4 OTH exome
AF:
0.131
GnomAD4 genome
AF:
0.136
AC:
20689
AN:
151776
Hom.:
1575
Cov.:
30
AF XY:
0.136
AC XY:
10062
AN XY:
74162
show subpopulations
Gnomad4 AFR
AF:
0.174
Gnomad4 AMR
AF:
0.102
Gnomad4 ASJ
AF:
0.184
Gnomad4 EAS
AF:
0.00194
Gnomad4 SAS
AF:
0.163
Gnomad4 FIN
AF:
0.140
Gnomad4 NFE
AF:
0.126
Gnomad4 OTH
AF:
0.133
Alfa
AF:
0.141
Hom.:
291
Bravo
AF:
0.135
Asia WGS
AF:
0.0770
AC:
270
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
15
DANN
Benign
0.67

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
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: rs12774010; hg19: chr10-50121425; API