rs11264422

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 0.479 in 152,164 control chromosomes in the GnomAD database, including 22,002 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 0.48 ( 22002 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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:
0.480
AC:
72965
AN:
152046
Hom.:
22001
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.119
Gnomad AMI
AF:
0.599
Gnomad AMR
AF:
0.568
Gnomad ASJ
AF:
0.647
Gnomad EAS
AF:
0.161
Gnomad SAS
AF:
0.540
Gnomad FIN
AF:
0.621
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.666
Gnomad OTH
AF:
0.521
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.479
AC:
72958
AN:
152164
Hom.:
22002
Cov.:
32
AF XY:
0.478
AC XY:
35574
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.118
Gnomad4 AMR
AF:
0.567
Gnomad4 ASJ
AF:
0.647
Gnomad4 EAS
AF:
0.161
Gnomad4 SAS
AF:
0.540
Gnomad4 FIN
AF:
0.621
Gnomad4 NFE
AF:
0.666
Gnomad4 OTH
AF:
0.526
Alfa
AF:
0.570
Hom.:
3486
Bravo
AF:
0.455
Asia WGS
AF:
0.334
AC:
1159
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
6.3
DANN
Benign
0.62

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: rs11264422; hg19: chr1-155907823; API