rs903514

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 0.361 in 151,968 control chromosomes in the GnomAD database, including 10,612 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 0.36 ( 10612 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0900
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=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.361
AC:
54851
AN:
151848
Hom.:
10615
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.225
Gnomad AMI
AF:
0.359
Gnomad AMR
AF:
0.506
Gnomad ASJ
AF:
0.382
Gnomad EAS
AF:
0.301
Gnomad SAS
AF:
0.327
Gnomad FIN
AF:
0.396
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.411
Gnomad OTH
AF:
0.388
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.361
AC:
54875
AN:
151968
Hom.:
10612
Cov.:
31
AF XY:
0.361
AC XY:
26809
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.225
Gnomad4 AMR
AF:
0.506
Gnomad4 ASJ
AF:
0.382
Gnomad4 EAS
AF:
0.302
Gnomad4 SAS
AF:
0.328
Gnomad4 FIN
AF:
0.396
Gnomad4 NFE
AF:
0.411
Gnomad4 OTH
AF:
0.384
Alfa
AF:
0.396
Hom.:
15916
Bravo
AF:
0.370
Asia WGS
AF:
0.313
AC:
1092
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.71
DANN
Benign
0.58

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: rs903514; hg19: chr11-44352394; API