11-92958366-T-C

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 0.467 in 151,984 control chromosomes in the GnomAD database, including 17,583 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 0.47 ( 17583 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.658
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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:
0.467
AC:
70895
AN:
151866
Hom.:
17547
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.645
Gnomad AMI
AF:
0.551
Gnomad AMR
AF:
0.349
Gnomad ASJ
AF:
0.366
Gnomad EAS
AF:
0.447
Gnomad SAS
AF:
0.472
Gnomad FIN
AF:
0.447
Gnomad MID
AF:
0.478
Gnomad NFE
AF:
0.394
Gnomad OTH
AF:
0.460
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.467
AC:
70989
AN:
151984
Hom.:
17583
Cov.:
32
AF XY:
0.467
AC XY:
34663
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.645
Gnomad4 AMR
AF:
0.348
Gnomad4 ASJ
AF:
0.366
Gnomad4 EAS
AF:
0.448
Gnomad4 SAS
AF:
0.472
Gnomad4 FIN
AF:
0.447
Gnomad4 NFE
AF:
0.394
Gnomad4 OTH
AF:
0.459
Alfa
AF:
0.405
Hom.:
29092
Bravo
AF:
0.466
Asia WGS
AF:
0.416
AC:
1447
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.25
DANN
Benign
0.52

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: rs2166706; hg19: chr11-92691532; API