11-35071523-A-G

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 0.506 in 152,056 control chromosomes in the GnomAD database, including 20,495 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 0.51 ( 20495 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.537
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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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:
0.506
AC:
76919
AN:
151938
Hom.:
20489
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.337
Gnomad AMI
AF:
0.567
Gnomad AMR
AF:
0.599
Gnomad ASJ
AF:
0.610
Gnomad EAS
AF:
0.754
Gnomad SAS
AF:
0.690
Gnomad FIN
AF:
0.514
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.548
Gnomad OTH
AF:
0.538
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.506
AC:
76942
AN:
152056
Hom.:
20495
Cov.:
32
AF XY:
0.512
AC XY:
38040
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.336
Gnomad4 AMR
AF:
0.600
Gnomad4 ASJ
AF:
0.610
Gnomad4 EAS
AF:
0.753
Gnomad4 SAS
AF:
0.689
Gnomad4 FIN
AF:
0.514
Gnomad4 NFE
AF:
0.548
Gnomad4 OTH
AF:
0.541
Alfa
AF:
0.543
Hom.:
12819
Bravo
AF:
0.502
Asia WGS
AF:
0.686
AC:
2381
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
13
DANN
Benign
0.81

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: rs2785197; hg19: chr11-35093070; API