rs2243307

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The variant allele was found at a frequency of 0.00515 in 137,730 control chromosomes in the GnomAD database, including 37 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 0.0051 ( 37 hom., cov: 25)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.56
Variant links:

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ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.09).
BS2
High Homozygotes in GnomAd4 at 37 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:
0.00515
AC:
709
AN:
137608
Hom.:
37
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.00165
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00377
Gnomad ASJ
AF:
0.000329
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000975
Gnomad FIN
AF:
0.00235
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00932
Gnomad OTH
AF:
0.00275
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00515
AC:
709
AN:
137730
Hom.:
37
Cov.:
25
AF XY:
0.00475
AC XY:
319
AN XY:
67174
show subpopulations
Gnomad4 AFR
AF:
0.00164
Gnomad4 AMR
AF:
0.00377
Gnomad4 ASJ
AF:
0.000329
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000976
Gnomad4 FIN
AF:
0.00235
Gnomad4 NFE
AF:
0.00932
Gnomad4 OTH
AF:
0.00272
Alfa
AF:
0.00563
Hom.:
5

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.56
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: rs2243307; hg19: chr5-132008272; API