rs12063780

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 0.135 in 152,154 control chromosomes in the GnomAD database, including 1,985 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 ( 1985 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.402
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.135
AC:
20573
AN:
152036
Hom.:
1978
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.273
Gnomad AMI
AF:
0.0680
Gnomad AMR
AF:
0.0898
Gnomad ASJ
AF:
0.124
Gnomad EAS
AF:
0.201
Gnomad SAS
AF:
0.130
Gnomad FIN
AF:
0.0599
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.0699
Gnomad OTH
AF:
0.144
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.135
AC:
20605
AN:
152154
Hom.:
1985
Cov.:
32
AF XY:
0.134
AC XY:
9935
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.273
Gnomad4 AMR
AF:
0.0898
Gnomad4 ASJ
AF:
0.124
Gnomad4 EAS
AF:
0.201
Gnomad4 SAS
AF:
0.130
Gnomad4 FIN
AF:
0.0599
Gnomad4 NFE
AF:
0.0699
Gnomad4 OTH
AF:
0.142
Alfa
AF:
0.103
Hom.:
156
Bravo
AF:
0.143
Asia WGS
AF:
0.185
AC:
644
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.3
DANN
Benign
0.49

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: rs12063780; hg19: chr1-207275294; API