chr15-96883135-G-A

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 0.221 in 152,036 control chromosomes in the GnomAD database, including 4,026 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 0.22 ( 4026 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539
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 = 0.27 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:
0.221
AC:
33646
AN:
151918
Hom.:
4028
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.155
Gnomad AMI
AF:
0.313
Gnomad AMR
AF:
0.183
Gnomad ASJ
AF:
0.301
Gnomad EAS
AF:
0.237
Gnomad SAS
AF:
0.189
Gnomad FIN
AF:
0.174
Gnomad MID
AF:
0.303
Gnomad NFE
AF:
0.273
Gnomad OTH
AF:
0.238
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.221
AC:
33654
AN:
152036
Hom.:
4026
Cov.:
32
AF XY:
0.218
AC XY:
16176
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.155
Gnomad4 AMR
AF:
0.183
Gnomad4 ASJ
AF:
0.301
Gnomad4 EAS
AF:
0.236
Gnomad4 SAS
AF:
0.188
Gnomad4 FIN
AF:
0.174
Gnomad4 NFE
AF:
0.273
Gnomad4 OTH
AF:
0.236
Alfa
AF:
0.252
Hom.:
4154
Bravo
AF:
0.219
Asia WGS
AF:
0.170
AC:
594
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
0.52
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: rs983188; hg19: chr15-97426365; API