rs7188230

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 0.303 in 151,802 control chromosomes in the GnomAD database, including 8,891 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 0.30 ( 8891 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.814
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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 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:
0.303
AC:
45939
AN:
151682
Hom.:
8872
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.550
Gnomad AMI
AF:
0.281
Gnomad AMR
AF:
0.184
Gnomad ASJ
AF:
0.235
Gnomad EAS
AF:
0.0299
Gnomad SAS
AF:
0.218
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.216
Gnomad OTH
AF:
0.275
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.303
AC:
46007
AN:
151802
Hom.:
8891
Cov.:
32
AF XY:
0.302
AC XY:
22438
AN XY:
74184
show subpopulations
Gnomad4 AFR
AF:
0.550
Gnomad4 AMR
AF:
0.184
Gnomad4 ASJ
AF:
0.235
Gnomad4 EAS
AF:
0.0300
Gnomad4 SAS
AF:
0.219
Gnomad4 FIN
AF:
0.272
Gnomad4 NFE
AF:
0.216
Gnomad4 OTH
AF:
0.273
Alfa
AF:
0.295
Hom.:
1524
Bravo
AF:
0.306
Asia WGS
AF:
0.146
AC:
510
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
5.5
DANN
Benign
0.42

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: rs7188230; hg19: chr16-55743767; API