12-61563638-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 0.447 in 151,774 control chromosomes in the GnomAD database, including 16,104 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 0.45 ( 16104 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.204
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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 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:
0.447
AC:
67779
AN:
151656
Hom.:
16105
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.275
Gnomad AMI
AF:
0.553
Gnomad AMR
AF:
0.524
Gnomad ASJ
AF:
0.511
Gnomad EAS
AF:
0.353
Gnomad SAS
AF:
0.439
Gnomad FIN
AF:
0.483
Gnomad MID
AF:
0.547
Gnomad NFE
AF:
0.530
Gnomad OTH
AF:
0.483
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.447
AC:
67794
AN:
151774
Hom.:
16104
Cov.:
32
AF XY:
0.446
AC XY:
33058
AN XY:
74158
show subpopulations
Gnomad4 AFR
AF:
0.275
Gnomad4 AMR
AF:
0.524
Gnomad4 ASJ
AF:
0.511
Gnomad4 EAS
AF:
0.352
Gnomad4 SAS
AF:
0.438
Gnomad4 FIN
AF:
0.483
Gnomad4 NFE
AF:
0.530
Gnomad4 OTH
AF:
0.478
Alfa
AF:
0.523
Hom.:
27535
Bravo
AF:
0.444
Asia WGS
AF:
0.415
AC:
1441
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.1
DANN
Benign
0.50

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: rs7296490; hg19: chr12-61957419; API