rs11037965

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 0.0991 in 152,226 control chromosomes in the GnomAD database, including 1,296 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 0.099 ( 1296 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.335
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.223 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:
0.0988
AC:
15034
AN:
152108
Hom.:
1282
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.190
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.229
Gnomad ASJ
AF:
0.0426
Gnomad EAS
AF:
0.0805
Gnomad SAS
AF:
0.0918
Gnomad FIN
AF:
0.00725
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0340
Gnomad OTH
AF:
0.110
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0991
AC:
15083
AN:
152226
Hom.:
1296
Cov.:
32
AF XY:
0.0994
AC XY:
7398
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.191
Gnomad4 AMR
AF:
0.229
Gnomad4 ASJ
AF:
0.0426
Gnomad4 EAS
AF:
0.0801
Gnomad4 SAS
AF:
0.0920
Gnomad4 FIN
AF:
0.00725
Gnomad4 NFE
AF:
0.0340
Gnomad4 OTH
AF:
0.110
Alfa
AF:
0.0743
Hom.:
287
Bravo
AF:
0.118
Asia WGS
AF:
0.101
AC:
354
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.83
DANN
Benign
0.71

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: rs11037965; hg19: chr11-44378156; API