rs916457

Positions:

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 0.0766 in 152,138 control chromosomes in the GnomAD database, including 544 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 0.077 ( 544 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08
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=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 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:
0.0765
AC:
11633
AN:
152026
Hom.:
541
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.102
Gnomad AMI
AF:
0.0352
Gnomad AMR
AF:
0.131
Gnomad ASJ
AF:
0.0539
Gnomad EAS
AF:
0.134
Gnomad SAS
AF:
0.105
Gnomad FIN
AF:
0.0238
Gnomad MID
AF:
0.0828
Gnomad NFE
AF:
0.0529
Gnomad OTH
AF:
0.0635
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0766
AC:
11659
AN:
152138
Hom.:
544
Cov.:
32
AF XY:
0.0777
AC XY:
5783
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.131
Gnomad4 ASJ
AF:
0.0539
Gnomad4 EAS
AF:
0.134
Gnomad4 SAS
AF:
0.105
Gnomad4 FIN
AF:
0.0238
Gnomad4 NFE
AF:
0.0529
Gnomad4 OTH
AF:
0.0671
Alfa
AF:
0.0614
Hom.:
41
Bravo
AF:
0.0806
Asia WGS
AF:
0.136
AC:
470
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
10
DANN
Benign
0.93

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: rs916457; hg19: chr11-637014; API