11-6735165-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000526769.3(ENSG00000291143):​n.91+11184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,996 control chromosomes in the GnomAD database, including 11,302 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 ( 11302 hom., cov: 32)

Consequence

ENSG00000291143
ENST00000526769.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.408
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000291143ENST00000526769.3 linkn.91+11184A>G intron_variant 1
ENSG00000291143ENST00000687034.2 linkn.149-1016A>G intron_variant
ENSG00000291143ENST00000702834.1 linkn.127-998A>G intron_variant
ENSG00000291143ENST00000702907.1 linkn.94-1024A>G intron_variant

Frequencies

GnomAD3 genomes
AF:
0.365
AC:
55369
AN:
151878
Hom.:
11303
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.179
Gnomad AMI
AF:
0.519
Gnomad AMR
AF:
0.348
Gnomad ASJ
AF:
0.413
Gnomad EAS
AF:
0.449
Gnomad SAS
AF:
0.313
Gnomad FIN
AF:
0.544
Gnomad MID
AF:
0.465
Gnomad NFE
AF:
0.445
Gnomad OTH
AF:
0.380
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.364
AC:
55388
AN:
151996
Hom.:
11302
Cov.:
32
AF XY:
0.368
AC XY:
27364
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.180
Gnomad4 AMR
AF:
0.347
Gnomad4 ASJ
AF:
0.413
Gnomad4 EAS
AF:
0.449
Gnomad4 SAS
AF:
0.314
Gnomad4 FIN
AF:
0.544
Gnomad4 NFE
AF:
0.445
Gnomad4 OTH
AF:
0.376
Alfa
AF:
0.406
Hom.:
6815
Bravo
AF:
0.342
Asia WGS
AF:
0.333
AC:
1158
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
4.5
DANN
Benign
0.23

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: rs951340; hg19: chr11-6756396; API