rs6016142

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The variant allele was found at a frequency of 0.0791 in 152,262 control chromosomes in the GnomAD database, including 595 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 0.079 ( 595 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.581
Variant links:

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ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.14).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 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:
0.0792
AC:
12048
AN:
152144
Hom.:
598
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0330
Gnomad AMI
AF:
0.147
Gnomad AMR
AF:
0.0735
Gnomad ASJ
AF:
0.112
Gnomad EAS
AF:
0.0764
Gnomad SAS
AF:
0.134
Gnomad FIN
AF:
0.0577
Gnomad MID
AF:
0.174
Gnomad NFE
AF:
0.105
Gnomad OTH
AF:
0.0952
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0791
AC:
12045
AN:
152262
Hom.:
595
Cov.:
33
AF XY:
0.0778
AC XY:
5795
AN XY:
74444
show subpopulations
Gnomad4 AFR
AF:
0.0331
Gnomad4 AMR
AF:
0.0735
Gnomad4 ASJ
AF:
0.112
Gnomad4 EAS
AF:
0.0764
Gnomad4 SAS
AF:
0.133
Gnomad4 FIN
AF:
0.0577
Gnomad4 NFE
AF:
0.105
Gnomad4 OTH
AF:
0.0928
Alfa
AF:
0.104
Hom.:
997
Bravo
AF:
0.0770
Asia WGS
AF:
0.0950
AC:
332
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.14
CADD
Benign
20
DANN
Benign
0.77

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: rs6016142; hg19: chr20-38300807; API