rs925587

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 0.3 in 152,042 control chromosomes in the GnomAD database, including 8,962 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 0.30 ( 8962 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25
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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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:
0.301
AC:
45656
AN:
151926
Hom.:
8961
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0828
Gnomad AMI
AF:
0.444
Gnomad AMR
AF:
0.266
Gnomad ASJ
AF:
0.385
Gnomad EAS
AF:
0.0435
Gnomad SAS
AF:
0.186
Gnomad FIN
AF:
0.473
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.435
Gnomad OTH
AF:
0.309
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.300
AC:
45650
AN:
152042
Hom.:
8962
Cov.:
32
AF XY:
0.297
AC XY:
22090
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.0827
Gnomad4 AMR
AF:
0.266
Gnomad4 ASJ
AF:
0.385
Gnomad4 EAS
AF:
0.0434
Gnomad4 SAS
AF:
0.186
Gnomad4 FIN
AF:
0.473
Gnomad4 NFE
AF:
0.435
Gnomad4 OTH
AF:
0.305
Alfa
AF:
0.383
Hom.:
2583
Bravo
AF:
0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
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: rs925587; hg19: chr10-48300663; API