rs10911628

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 0.0917 in 152,198 control chromosomes in the GnomAD database, including 852 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 0.092 ( 852 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.234
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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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:
0.0916
AC:
13928
AN:
152080
Hom.:
851
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.174
Gnomad AMI
AF:
0.0603
Gnomad AMR
AF:
0.0755
Gnomad ASJ
AF:
0.0874
Gnomad EAS
AF:
0.0483
Gnomad SAS
AF:
0.0516
Gnomad FIN
AF:
0.0164
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.0630
Gnomad OTH
AF:
0.0970
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0917
AC:
13954
AN:
152198
Hom.:
852
Cov.:
32
AF XY:
0.0880
AC XY:
6548
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.174
Gnomad4 AMR
AF:
0.0755
Gnomad4 ASJ
AF:
0.0874
Gnomad4 EAS
AF:
0.0482
Gnomad4 SAS
AF:
0.0514
Gnomad4 FIN
AF:
0.0164
Gnomad4 NFE
AF:
0.0630
Gnomad4 OTH
AF:
0.0965
Alfa
AF:
0.0689
Hom.:
369
Bravo
AF:
0.101
Asia WGS
AF:
0.0590
AC:
205
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
4.2
DANN
Benign
0.61

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: rs10911628; hg19: chr1-184649503; API