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GeneBe

rs2275913

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The variant allele was found at a frequency of 0.284 in 152006 control chromosomes in the gnomAD Genomes database, including 7472 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 7472 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.334

Links

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 6:52186235-G>A is Benign according to our data. Variant chr6-52186235-G-A is described in ClinVar as [Benign]. Clinvar id is 1278437. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 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:
0.284
AC:
43152
AN:
152006
Hom.:
7472
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0959
Gnomad AMI
AF:
0.320
Gnomad AMR
AF:
0.242
Gnomad ASJ
AF:
0.293
Gnomad EAS
AF:
0.466
Gnomad SAS
AF:
0.383
Gnomad FIN
AF:
0.472
Gnomad MID
AF:
0.277
Gnomad NFE
AF:
0.357
Gnomad OTH
AF:
0.288
Alfa
AF:
0.334
Hom.:
6199
Bravo
AF:
0.255
Asia WGS
AF:
0.372
AC:
1293
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 12, 2018This variant is associated with the following publications: (PMID: 22537748, 21672939, 22028838, 29372577, 25595174, 29985710, 23778030) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
1.1
Dann
Benign
0.75

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: rs2275913; hg19: chr6-52051033;