rs10513909

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 0.171 in 151,772 control chromosomes in the GnomAD database, including 3,047 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 0.17 ( 3047 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0460
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 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:
0.171
AC:
25901
AN:
151654
Hom.:
3037
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.339
Gnomad AMI
AF:
0.0833
Gnomad AMR
AF:
0.113
Gnomad ASJ
AF:
0.123
Gnomad EAS
AF:
0.0976
Gnomad SAS
AF:
0.151
Gnomad FIN
AF:
0.122
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.101
Gnomad OTH
AF:
0.145
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.171
AC:
25948
AN:
151772
Hom.:
3047
Cov.:
31
AF XY:
0.171
AC XY:
12670
AN XY:
74144
show subpopulations
Gnomad4 AFR
AF:
0.339
Gnomad4 AMR
AF:
0.113
Gnomad4 ASJ
AF:
0.123
Gnomad4 EAS
AF:
0.0974
Gnomad4 SAS
AF:
0.151
Gnomad4 FIN
AF:
0.122
Gnomad4 NFE
AF:
0.101
Gnomad4 OTH
AF:
0.147
Alfa
AF:
0.101
Hom.:
744
Bravo
AF:
0.177
Asia WGS
AF:
0.140
AC:
487
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.6
DANN
Benign
0.64

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: rs10513909; hg19: chr18-20072571; API