rs1918526

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 0.89 in 152,242 control chromosomes in the GnomAD database, including 62,054 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 0.89 ( 62054 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.556
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.891
AC:
135467
AN:
152124
Hom.:
62032
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.649
Gnomad AMI
AF:
0.992
Gnomad AMR
AF:
0.946
Gnomad ASJ
AF:
0.974
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.934
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.905
Gnomad NFE
AF:
0.991
Gnomad OTH
AF:
0.899
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.890
AC:
135544
AN:
152242
Hom.:
62054
Cov.:
33
AF XY:
0.894
AC XY:
66528
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.649
Gnomad4 AMR
AF:
0.947
Gnomad4 ASJ
AF:
0.974
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.934
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.991
Gnomad4 OTH
AF:
0.900
Alfa
AF:
0.918
Hom.:
10718
Bravo
AF:
0.875
Asia WGS
AF:
0.945
AC:
3286
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.43
DANN
Benign
0.39

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: rs1918526; hg19: chr7-115138008; API