rs10911902

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 0.137 in 152,078 control chromosomes in the GnomAD database, including 1,825 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 0.14 ( 1825 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.230
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 (SAS) allele frequency at 95% confidence interval = 0.188 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:
0.137
AC:
20814
AN:
151960
Hom.:
1826
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0337
Gnomad AMI
AF:
0.160
Gnomad AMR
AF:
0.121
Gnomad ASJ
AF:
0.103
Gnomad EAS
AF:
0.143
Gnomad SAS
AF:
0.197
Gnomad FIN
AF:
0.213
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.189
Gnomad OTH
AF:
0.107
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.137
AC:
20810
AN:
152078
Hom.:
1825
Cov.:
32
AF XY:
0.138
AC XY:
10260
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.0336
Gnomad4 AMR
AF:
0.121
Gnomad4 ASJ
AF:
0.103
Gnomad4 EAS
AF:
0.144
Gnomad4 SAS
AF:
0.198
Gnomad4 FIN
AF:
0.213
Gnomad4 NFE
AF:
0.189
Gnomad4 OTH
AF:
0.106
Alfa
AF:
0.172
Hom.:
3266
Bravo
AF:
0.123
Asia WGS
AF:
0.148
AC:
517
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
4.7
DANN
Benign
0.28

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: rs10911902; hg19: chr1-186632317; API