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GeneBe

rs1800775

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 0.522 in 151974 control chromosomes in the gnomAD Genomes database, including 20854 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 0.52 ( 20854 hom., cov: 33)
Exomes 𝑓: 0.51 ( 22587 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.582 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:
0.522
AC:
79285
AN:
151974
Hom.:
20854
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.575
Gnomad AMI
AF:
0.653
Gnomad AMR
AF:
0.506
Gnomad ASJ
AF:
0.504
Gnomad EAS
AF:
0.499
Gnomad SAS
AF:
0.601
Gnomad FIN
AF:
0.509
Gnomad MID
AF:
0.509
Gnomad NFE
AF:
0.490
Gnomad OTH
AF:
0.502
GnomAD3 exomes
AF:
0.508
AC:
88585
AN:
174424
Hom.:
22587
AF XY:
0.511
AC XY:
48698
AN XY:
95346
show subpopulations
Gnomad AFR exome
AF:
0.558
Gnomad AMR exome
AF:
0.528
Gnomad ASJ exome
AF:
0.513
Gnomad EAS exome
AF:
0.491
Gnomad SAS exome
AF:
0.592
Gnomad FIN exome
AF:
0.467
Gnomad NFE exome
AF:
0.473
Gnomad OTH exome
AF:
0.500
GnomAD4 exome
AF:
0.512
AC:
168449
AN:
328950
Hom.:
43647
AF XY:
0.518
AC XY:
97232
AN XY:
187742
show subpopulations
Gnomad4 AFR exome
AF:
0.567
Gnomad4 AMR exome
AF:
0.528
Gnomad4 ASJ exome
AF:
0.511
Gnomad4 EAS exome
AF:
0.500
Gnomad4 SAS exome
AF:
0.598
Gnomad4 FIN exome
AF:
0.490
Gnomad4 NFE exome
AF:
0.479
Gnomad4 OTH exome
AF:
0.504
Alfa
AF:
0.497
Hom.:
41336
Bravo
AF:
0.522
Asia WGS
AF:
0.546
AC:
1902
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
1.1
Dann
Benign
0.66

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: rs1800775; hg19: chr16-56995236; COSMIC: COSV52363979;