11-62028114-T-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 0.0746 in 152,040 control chromosomes in the GnomAD database, including 1,046 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 0.075 ( 1046 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.214
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 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:
0.0745
AC:
11312
AN:
151922
Hom.:
1038
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0619
Gnomad AMI
AF:
0.00440
Gnomad AMR
AF:
0.200
Gnomad ASJ
AF:
0.0118
Gnomad EAS
AF:
0.447
Gnomad SAS
AF:
0.0974
Gnomad FIN
AF:
0.0536
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.0317
Gnomad OTH
AF:
0.0775
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0746
AC:
11339
AN:
152040
Hom.:
1046
Cov.:
32
AF XY:
0.0809
AC XY:
6015
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.0620
Gnomad4 AMR
AF:
0.201
Gnomad4 ASJ
AF:
0.0118
Gnomad4 EAS
AF:
0.448
Gnomad4 SAS
AF:
0.0979
Gnomad4 FIN
AF:
0.0536
Gnomad4 NFE
AF:
0.0317
Gnomad4 OTH
AF:
0.0762
Alfa
AF:
0.0520
Hom.:
65
Bravo
AF:
0.0921
Asia WGS
AF:
0.199
AC:
691
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
4.2
DANN
Benign
0.28

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: rs11230874; hg19: chr11-61795586; API