rs11265260

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 0.0693 in 152,228 control chromosomes in the GnomAD database, including 446 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 0.069 ( 446 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.748
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 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:
0.0694
AC:
10551
AN:
152110
Hom.:
444
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0701
Gnomad AMI
AF:
0.0417
Gnomad AMR
AF:
0.0566
Gnomad ASJ
AF:
0.112
Gnomad EAS
AF:
0.152
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.0651
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.0607
Gnomad OTH
AF:
0.0861
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0693
AC:
10557
AN:
152228
Hom.:
446
Cov.:
32
AF XY:
0.0699
AC XY:
5206
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0704
Gnomad4 AMR
AF:
0.0565
Gnomad4 ASJ
AF:
0.112
Gnomad4 EAS
AF:
0.152
Gnomad4 SAS
AF:
0.108
Gnomad4 FIN
AF:
0.0651
Gnomad4 NFE
AF:
0.0607
Gnomad4 OTH
AF:
0.0866
Alfa
AF:
0.0664
Hom.:
813
Bravo
AF:
0.0684
Asia WGS
AF:
0.0900
AC:
311
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
7.3
DANN
Benign
0.63

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: rs11265260; hg19: chr1-159700039; API