rs7759127

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 0.113 in 152,144 control chromosomes in the GnomAD database, including 1,036 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 0.11 ( 1036 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.846
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 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:
0.113
AC:
17243
AN:
152026
Hom.:
1036
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.112
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.119
Gnomad ASJ
AF:
0.150
Gnomad EAS
AF:
0.105
Gnomad SAS
AF:
0.0674
Gnomad FIN
AF:
0.0524
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.124
Gnomad OTH
AF:
0.121
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.113
AC:
17242
AN:
152144
Hom.:
1036
Cov.:
32
AF XY:
0.108
AC XY:
8037
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.118
Gnomad4 ASJ
AF:
0.150
Gnomad4 EAS
AF:
0.105
Gnomad4 SAS
AF:
0.0671
Gnomad4 FIN
AF:
0.0524
Gnomad4 NFE
AF:
0.124
Gnomad4 OTH
AF:
0.120
Alfa
AF:
0.128
Hom.:
115
Bravo
AF:
0.120
Asia WGS
AF:
0.0870
AC:
305
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
7.9
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: rs7759127; hg19: chr6-31240988; API