chr18-78703038-G-A

Variant summary

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

The variant allele was found at a frequency of 0.281 in 152,040 control chromosomes in the GnomAD database, including 6,480 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 0.28 ( 6480 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.291
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.281
AC:
42749
AN:
151922
Hom.:
6477
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.264
Gnomad AMI
AF:
0.339
Gnomad AMR
AF:
0.297
Gnomad ASJ
AF:
0.231
Gnomad EAS
AF:
0.624
Gnomad SAS
AF:
0.375
Gnomad FIN
AF:
0.268
Gnomad MID
AF:
0.226
Gnomad NFE
AF:
0.260
Gnomad OTH
AF:
0.262
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.281
AC:
42781
AN:
152040
Hom.:
6480
Cov.:
33
AF XY:
0.285
AC XY:
21163
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.264
Gnomad4 AMR
AF:
0.298
Gnomad4 ASJ
AF:
0.231
Gnomad4 EAS
AF:
0.624
Gnomad4 SAS
AF:
0.375
Gnomad4 FIN
AF:
0.268
Gnomad4 NFE
AF:
0.260
Gnomad4 OTH
AF:
0.263
Alfa
AF:
0.270
Hom.:
3187
Bravo
AF:
0.282
Asia WGS
AF:
0.488
AC:
1693
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
6.6
DANN
Benign
0.79

Splicing

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: rs11659609; hg19: chr18-76463038; API