rs7586540

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 0.893 in 152,120 control chromosomes in the GnomAD database, including 60,849 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 ( 60849 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.893
AC:
135694
AN:
152002
Hom.:
60787
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.943
Gnomad AMI
AF:
0.823
Gnomad AMR
AF:
0.898
Gnomad ASJ
AF:
0.840
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.947
Gnomad FIN
AF:
0.899
Gnomad MID
AF:
0.820
Gnomad NFE
AF:
0.852
Gnomad OTH
AF:
0.870
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.893
AC:
135816
AN:
152120
Hom.:
60849
Cov.:
30
AF XY:
0.897
AC XY:
66679
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.943
Gnomad4 AMR
AF:
0.899
Gnomad4 ASJ
AF:
0.840
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.946
Gnomad4 FIN
AF:
0.899
Gnomad4 NFE
AF:
0.852
Gnomad4 OTH
AF:
0.872
Alfa
AF:
0.867
Hom.:
36160
Bravo
AF:
0.894
Asia WGS
AF:
0.975
AC:
3389
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.6
DANN
Benign
0.43

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: rs7586540; hg19: chr2-6052751; API