GeneBe

chr8-7893686-A-C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.000040 ( 0 hom., cov: 17)
Failed GnomAD Quality Control

Consequence

LOC124901865
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.284

Publications

2 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124901865 n.7893686A>C intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0000395
AC:
4
AN:
101222
Hom.:
0
Cov.:
17
show subpopulations
Gnomad AFR
AF:
0.000152
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000395
AC:
4
AN:
101222
Hom.:
0
Cov.:
17
AF XY:
0.0000204
AC XY:
1
AN XY:
49044
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.000152
AC:
4
AN:
26346
American (AMR)
AF:
0.00
AC:
0
AN:
10560
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2392
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2510
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2672
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
7590
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
194
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
46962
Other (OTH)
AF:
0.00
AC:
0
AN:
1360
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.263
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
3.9
DANN
Benign
0.18
PhyloP100
-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs3762040; hg19: chr8-7751208; API