rs11894053

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 0.257 in 152,180 control chromosomes in the GnomAD database, including 5,392 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 0.26 ( 5392 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.109
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=-0.77).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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:
0.257
AC:
39125
AN:
152062
Hom.:
5388
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.323
Gnomad AMI
AF:
0.454
Gnomad AMR
AF:
0.187
Gnomad ASJ
AF:
0.321
Gnomad EAS
AF:
0.103
Gnomad SAS
AF:
0.282
Gnomad FIN
AF:
0.308
Gnomad MID
AF:
0.358
Gnomad NFE
AF:
0.229
Gnomad OTH
AF:
0.263
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.257
AC:
39158
AN:
152180
Hom.:
5392
Cov.:
33
AF XY:
0.260
AC XY:
19347
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.323
Gnomad4 AMR
AF:
0.187
Gnomad4 ASJ
AF:
0.321
Gnomad4 EAS
AF:
0.102
Gnomad4 SAS
AF:
0.283
Gnomad4 FIN
AF:
0.308
Gnomad4 NFE
AF:
0.229
Gnomad4 OTH
AF:
0.265
Alfa
AF:
0.234
Hom.:
733
Bravo
AF:
0.251
Asia WGS
AF:
0.205
AC:
716
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
3.4
DANN
Benign
0.78

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: rs11894053; hg19: chr2-42229545; API