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GeneBe

rs1800587

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 0.317 in 152,114 control chromosomes in the GnomAD database, including 7,960 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 0.32 ( 7960 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.170
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 (AFR) allele frequency at 95% confidence interval = 0.387 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:
0.317
AC:
48202
AN:
151996
Hom.:
7944
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.392
Gnomad AMI
AF:
0.407
Gnomad AMR
AF:
0.291
Gnomad ASJ
AF:
0.343
Gnomad EAS
AF:
0.0787
Gnomad SAS
AF:
0.291
Gnomad FIN
AF:
0.316
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.308
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.317
AC:
48262
AN:
152114
Hom.:
7960
Cov.:
33
AF XY:
0.317
AC XY:
23570
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.392
Gnomad4 AMR
AF:
0.291
Gnomad4 ASJ
AF:
0.343
Gnomad4 EAS
AF:
0.0787
Gnomad4 SAS
AF:
0.291
Gnomad4 FIN
AF:
0.316
Gnomad4 NFE
AF:
0.295
Gnomad4 OTH
AF:
0.306
Alfa
AF:
0.285
Hom.:
6471
Bravo
AF:
0.316
Asia WGS
AF:
0.212
AC:
741
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
2.6
Dann
Benign
0.38

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: rs1800587; hg19: chr2-113542960; API