rs7752279

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 0.593 in 152,066 control chromosomes in the GnomAD database, including 29,775 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 0.59 ( 29775 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.174
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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:
0.592
AC:
89998
AN:
151948
Hom.:
29716
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.891
Gnomad AMI
AF:
0.681
Gnomad AMR
AF:
0.612
Gnomad ASJ
AF:
0.409
Gnomad EAS
AF:
0.541
Gnomad SAS
AF:
0.657
Gnomad FIN
AF:
0.463
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.433
Gnomad OTH
AF:
0.588
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.593
AC:
90120
AN:
152066
Hom.:
29775
Cov.:
32
AF XY:
0.595
AC XY:
44230
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.892
Gnomad4 AMR
AF:
0.612
Gnomad4 ASJ
AF:
0.409
Gnomad4 EAS
AF:
0.542
Gnomad4 SAS
AF:
0.657
Gnomad4 FIN
AF:
0.463
Gnomad4 NFE
AF:
0.433
Gnomad4 OTH
AF:
0.587
Alfa
AF:
0.520
Hom.:
2824
Bravo
AF:
0.614
Asia WGS
AF:
0.615
AC:
2140
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.2
DANN
Benign
0.69

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: rs7752279; hg19: chr6-132112335; API