rs7894582

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 0.0652 in 152,182 control chromosomes in the GnomAD database, including 427 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 0.065 ( 427 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.262
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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 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:
0.0652
AC:
9907
AN:
152064
Hom.:
423
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.120
Gnomad AMI
AF:
0.00658
Gnomad AMR
AF:
0.0356
Gnomad ASJ
AF:
0.0360
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.0270
Gnomad FIN
AF:
0.0839
Gnomad MID
AF:
0.0570
Gnomad NFE
AF:
0.0457
Gnomad OTH
AF:
0.0512
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0652
AC:
9929
AN:
152182
Hom.:
427
Cov.:
32
AF XY:
0.0651
AC XY:
4844
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.120
Gnomad4 AMR
AF:
0.0355
Gnomad4 ASJ
AF:
0.0360
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.0270
Gnomad4 FIN
AF:
0.0839
Gnomad4 NFE
AF:
0.0457
Gnomad4 OTH
AF:
0.0521
Alfa
AF:
0.0451
Hom.:
254
Bravo
AF:
0.0642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.77
DANN
Benign
0.51

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: rs7894582; hg19: chr10-115704458; API