11-114320294-A-G

Variant summary

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

The ENST00000544925.1(ENSG00000256947):​n.50+36228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,040 control chromosomes in the GnomAD database, including 32,619 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 0.65 ( 32619 hom., cov: 32)

Consequence

ENSG00000256947
ENST00000544925.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.986
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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
ENSG00000256947ENST00000544925.1 linkn.50+36228T>C intron_variant Intron 1 of 2 5

Frequencies

GnomAD3 genomes
AF:
0.651
AC:
98917
AN:
151922
Hom.:
32589
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.728
Gnomad AMI
AF:
0.591
Gnomad AMR
AF:
0.669
Gnomad ASJ
AF:
0.492
Gnomad EAS
AF:
0.504
Gnomad SAS
AF:
0.521
Gnomad FIN
AF:
0.746
Gnomad MID
AF:
0.570
Gnomad NFE
AF:
0.616
Gnomad OTH
AF:
0.628
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.651
AC:
99000
AN:
152040
Hom.:
32619
Cov.:
32
AF XY:
0.653
AC XY:
48503
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.728
Gnomad4 AMR
AF:
0.670
Gnomad4 ASJ
AF:
0.492
Gnomad4 EAS
AF:
0.504
Gnomad4 SAS
AF:
0.520
Gnomad4 FIN
AF:
0.746
Gnomad4 NFE
AF:
0.616
Gnomad4 OTH
AF:
0.626
Alfa
AF:
0.603
Hom.:
58670
Bravo
AF:
0.651
Asia WGS
AF:
0.575
AC:
2001
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.7
DANN
Benign
0.59

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: rs2847476; hg19: chr11-114191016; API