8-49761210-G-C

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 0.684 in 151,864 control chromosomes in the GnomAD database, including 39,596 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 0.68 ( 39596 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00400
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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:
0.684
AC:
103794
AN:
151746
Hom.:
39598
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.316
Gnomad AMI
AF:
0.883
Gnomad AMR
AF:
0.748
Gnomad ASJ
AF:
0.763
Gnomad EAS
AF:
0.871
Gnomad SAS
AF:
0.782
Gnomad FIN
AF:
0.866
Gnomad MID
AF:
0.707
Gnomad NFE
AF:
0.837
Gnomad OTH
AF:
0.691
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.684
AC:
103805
AN:
151864
Hom.:
39596
Cov.:
30
AF XY:
0.689
AC XY:
51096
AN XY:
74206
show subpopulations
Gnomad4 AFR
AF:
0.315
Gnomad4 AMR
AF:
0.748
Gnomad4 ASJ
AF:
0.763
Gnomad4 EAS
AF:
0.871
Gnomad4 SAS
AF:
0.781
Gnomad4 FIN
AF:
0.866
Gnomad4 NFE
AF:
0.837
Gnomad4 OTH
AF:
0.692
Alfa
AF:
0.700
Hom.:
2785
Bravo
AF:
0.660
Asia WGS
AF:
0.768
AC:
2670
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.87
DANN
Benign
0.37

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: rs7821848; hg19: chr8-50673770; API