rs11913200

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 0.275 in 152,112 control chromosomes in the GnomAD database, including 6,601 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 0.27 ( 6601 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96
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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 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:
0.275
AC:
41725
AN:
151994
Hom.:
6582
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.417
Gnomad AMI
AF:
0.146
Gnomad AMR
AF:
0.229
Gnomad ASJ
AF:
0.155
Gnomad EAS
AF:
0.375
Gnomad SAS
AF:
0.331
Gnomad FIN
AF:
0.229
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.202
Gnomad OTH
AF:
0.256
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.275
AC:
41796
AN:
152112
Hom.:
6601
Cov.:
33
AF XY:
0.275
AC XY:
20464
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.418
Gnomad4 AMR
AF:
0.229
Gnomad4 ASJ
AF:
0.155
Gnomad4 EAS
AF:
0.375
Gnomad4 SAS
AF:
0.331
Gnomad4 FIN
AF:
0.229
Gnomad4 NFE
AF:
0.202
Gnomad4 OTH
AF:
0.260
Alfa
AF:
0.218
Hom.:
6071
Bravo
AF:
0.279
Asia WGS
AF:
0.396
AC:
1377
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.30
DANN
Benign
0.54

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: rs11913200; hg19: chr22-45828546; API