18-57180074-T-G

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 0.37 in 152,042 control chromosomes in the GnomAD database, including 11,435 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 0.37 ( 11435 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.565
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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:
0.369
AC:
56118
AN:
151924
Hom.:
11404
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.547
Gnomad AMI
AF:
0.210
Gnomad AMR
AF:
0.298
Gnomad ASJ
AF:
0.287
Gnomad EAS
AF:
0.339
Gnomad SAS
AF:
0.381
Gnomad FIN
AF:
0.349
Gnomad MID
AF:
0.316
Gnomad NFE
AF:
0.290
Gnomad OTH
AF:
0.319
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.370
AC:
56197
AN:
152042
Hom.:
11435
Cov.:
32
AF XY:
0.371
AC XY:
27549
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.548
Gnomad4 AMR
AF:
0.298
Gnomad4 ASJ
AF:
0.287
Gnomad4 EAS
AF:
0.340
Gnomad4 SAS
AF:
0.382
Gnomad4 FIN
AF:
0.349
Gnomad4 NFE
AF:
0.290
Gnomad4 OTH
AF:
0.316
Alfa
AF:
0.256
Hom.:
1235
Bravo
AF:
0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.1
DANN
Benign
0.63

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: rs12605509; hg19: chr18-54847305; API