rs7295750

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 0.662 in 152,148 control chromosomes in the GnomAD database, including 33,598 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 0.66 ( 33598 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.137
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=-0.67).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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:
0.662
AC:
100665
AN:
152030
Hom.:
33553
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.640
Gnomad AMI
AF:
0.548
Gnomad AMR
AF:
0.665
Gnomad ASJ
AF:
0.580
Gnomad EAS
AF:
0.941
Gnomad SAS
AF:
0.642
Gnomad FIN
AF:
0.674
Gnomad MID
AF:
0.604
Gnomad NFE
AF:
0.659
Gnomad OTH
AF:
0.652
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.662
AC:
100767
AN:
152148
Hom.:
33598
Cov.:
33
AF XY:
0.666
AC XY:
49584
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.641
Gnomad4 AMR
AF:
0.665
Gnomad4 ASJ
AF:
0.580
Gnomad4 EAS
AF:
0.942
Gnomad4 SAS
AF:
0.644
Gnomad4 FIN
AF:
0.674
Gnomad4 NFE
AF:
0.659
Gnomad4 OTH
AF:
0.655
Alfa
AF:
0.651
Hom.:
14605
Bravo
AF:
0.662
Asia WGS
AF:
0.765
AC:
2661
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
0.70
DANN
Benign
0.81

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: rs7295750; hg19: chr12-107537671; API