rs62094879

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 0.143 in 151,850 control chromosomes in the GnomAD database, including 1,840 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 ( 1840 hom., cov: 29)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.136
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 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:
0.143
AC:
21714
AN:
151730
Hom.:
1839
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.0947
Gnomad AMI
AF:
0.131
Gnomad AMR
AF:
0.106
Gnomad ASJ
AF:
0.294
Gnomad EAS
AF:
0.00233
Gnomad SAS
AF:
0.0989
Gnomad FIN
AF:
0.114
Gnomad MID
AF:
0.218
Gnomad NFE
AF:
0.191
Gnomad OTH
AF:
0.155
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.143
AC:
21717
AN:
151850
Hom.:
1840
Cov.:
29
AF XY:
0.136
AC XY:
10074
AN XY:
74182
show subpopulations
Gnomad4 AFR
AF:
0.0948
Gnomad4 AMR
AF:
0.105
Gnomad4 ASJ
AF:
0.294
Gnomad4 EAS
AF:
0.00233
Gnomad4 SAS
AF:
0.0984
Gnomad4 FIN
AF:
0.114
Gnomad4 NFE
AF:
0.191
Gnomad4 OTH
AF:
0.153
Alfa
AF:
0.165
Hom.:
280
Bravo
AF:
0.143
Asia WGS
AF:
0.0620
AC:
217
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.0
DANN
Benign
0.69

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: rs62094879; hg19: chr18-55496305; API