rs7795288

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 0.343 in 151,996 control chromosomes in the GnomAD database, including 12,188 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 0.34 ( 12188 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.225
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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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:
0.343
AC:
52081
AN:
151876
Hom.:
12165
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.599
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.399
Gnomad ASJ
AF:
0.193
Gnomad EAS
AF:
0.766
Gnomad SAS
AF:
0.402
Gnomad FIN
AF:
0.138
Gnomad MID
AF:
0.264
Gnomad NFE
AF:
0.180
Gnomad OTH
AF:
0.321
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.343
AC:
52156
AN:
151996
Hom.:
12188
Cov.:
31
AF XY:
0.347
AC XY:
25797
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.599
Gnomad4 AMR
AF:
0.400
Gnomad4 ASJ
AF:
0.193
Gnomad4 EAS
AF:
0.766
Gnomad4 SAS
AF:
0.402
Gnomad4 FIN
AF:
0.138
Gnomad4 NFE
AF:
0.180
Gnomad4 OTH
AF:
0.322
Alfa
AF:
0.139
Hom.:
2643
Bravo
AF:
0.374
Asia WGS
AF:
0.549
AC:
1910
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.4
DANN
Benign
0.62

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: rs7795288; hg19: chr7-44823524; API