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rs1800750

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2

The variant allele was found at a frequency of 0.0161 in 152172 control chromosomes in the gnomAD Genomes database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.016 ( 35 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: 0.557

Links

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ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.0161 (2453/152172) while in subpopulation AMR AF= 0.0257 (392/15272). AF 95% confidence interval is 0.0236. There are 35 homozygotes in gnomad. There are 1161 alleles in male gnomad subpopulation. Median coverage is 31. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
?
High Homozygotes in GnomAd at 35 gene

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:
0.0161
AC:
2453
AN:
152172
Hom.:
35
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0208
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0257
Gnomad ASJ
AF:
0.0228
Gnomad EAS
AF:
0.00250
Gnomad SAS
AF:
0.00310
Gnomad FIN
AF:
0.00160
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.0147
Gnomad OTH
AF:
0.0307
GnomAD4 exome
AF:
0.0121
AC:
3634
AN:
301124
Hom.:
45
AF XY:
0.0112
AC XY:
1916
AN XY:
171752
show subpopulations
Gnomad4 AFR exome
AF:
0.0191
Gnomad4 AMR exome
AF:
0.0229
Gnomad4 ASJ exome
AF:
0.0228
Gnomad4 EAS exome
AF:
0.000323
Gnomad4 SAS exome
AF:
0.00546
Gnomad4 FIN exome
AF:
0.00331
Gnomad4 NFE exome
AF:
0.0126
Gnomad4 OTH exome
AF:
0.0148
Alfa
AF:
0.0157
Hom.:
38
Bravo
AF:
0.0179
Asia WGS
AF:
0.00577
AC:
20
AN:
3478

ClinVar

Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Malaria, cerebral, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJun 01, 1999- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
8.0
Dann
Benign
0.68

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: rs1800750; hg19: chr6-31542963; API