18-62393502-A-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 0.558 in 151,996 control chromosomes in the GnomAD database, including 24,372 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 0.56 ( 24372 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 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:
0.559
AC:
84832
AN:
151878
Hom.:
24366
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.606
Gnomad AMI
AF:
0.582
Gnomad AMR
AF:
0.545
Gnomad ASJ
AF:
0.609
Gnomad EAS
AF:
0.240
Gnomad SAS
AF:
0.563
Gnomad FIN
AF:
0.417
Gnomad MID
AF:
0.722
Gnomad NFE
AF:
0.574
Gnomad OTH
AF:
0.595
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.558
AC:
84871
AN:
151996
Hom.:
24372
Cov.:
31
AF XY:
0.549
AC XY:
40761
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.605
Gnomad4 AMR
AF:
0.544
Gnomad4 ASJ
AF:
0.609
Gnomad4 EAS
AF:
0.239
Gnomad4 SAS
AF:
0.563
Gnomad4 FIN
AF:
0.417
Gnomad4 NFE
AF:
0.574
Gnomad4 OTH
AF:
0.592
Alfa
AF:
0.572
Hom.:
57119
Bravo
AF:
0.568
Asia WGS
AF:
0.404
AC:
1408
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.86
DANN
Benign
0.40

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: rs2957128; hg19: chr18-60060735; API