rs714552

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 0.645 in 152,134 control chromosomes in the GnomAD database, including 33,063 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 0.65 ( 33063 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00900
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 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:
0.645
AC:
98037
AN:
152014
Hom.:
33012
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.808
Gnomad AMI
AF:
0.664
Gnomad AMR
AF:
0.474
Gnomad ASJ
AF:
0.692
Gnomad EAS
AF:
0.279
Gnomad SAS
AF:
0.613
Gnomad FIN
AF:
0.569
Gnomad MID
AF:
0.699
Gnomad NFE
AF:
0.623
Gnomad OTH
AF:
0.635
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.645
AC:
98142
AN:
152134
Hom.:
33063
Cov.:
33
AF XY:
0.638
AC XY:
47461
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.809
Gnomad4 AMR
AF:
0.473
Gnomad4 ASJ
AF:
0.692
Gnomad4 EAS
AF:
0.279
Gnomad4 SAS
AF:
0.613
Gnomad4 FIN
AF:
0.569
Gnomad4 NFE
AF:
0.623
Gnomad4 OTH
AF:
0.635
Alfa
AF:
0.640
Hom.:
3931
Bravo
AF:
0.639
Asia WGS
AF:
0.454
AC:
1582
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.2
DANN
Benign
0.54

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: rs714552; hg19: chr8-97183442; API