rs7821178

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 0.39 in 151,836 control chromosomes in the GnomAD database, including 12,114 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 0.39 ( 12114 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.635
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 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:
0.389
AC:
59073
AN:
151718
Hom.:
12072
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.497
Gnomad AMI
AF:
0.484
Gnomad AMR
AF:
0.378
Gnomad ASJ
AF:
0.325
Gnomad EAS
AF:
0.450
Gnomad SAS
AF:
0.471
Gnomad FIN
AF:
0.263
Gnomad MID
AF:
0.408
Gnomad NFE
AF:
0.337
Gnomad OTH
AF:
0.392
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.390
AC:
59171
AN:
151836
Hom.:
12114
Cov.:
32
AF XY:
0.391
AC XY:
28994
AN XY:
74170
show subpopulations
Gnomad4 AFR
AF:
0.498
Gnomad4 AMR
AF:
0.378
Gnomad4 ASJ
AF:
0.325
Gnomad4 EAS
AF:
0.451
Gnomad4 SAS
AF:
0.471
Gnomad4 FIN
AF:
0.263
Gnomad4 NFE
AF:
0.337
Gnomad4 OTH
AF:
0.394
Alfa
AF:
0.330
Hom.:
8842
Bravo
AF:
0.400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.35
DANN
Benign
0.29

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: rs7821178; hg19: chr8-78093837; API