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GeneBe

rs10513430

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 0.0825 in 152,068 control chromosomes in the GnomAD database, including 1,150 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 0.083 ( 1150 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0180
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 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:
0.0824
AC:
12520
AN:
151950
Hom.:
1144
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.224
Gnomad AMI
AF:
0.0154
Gnomad AMR
AF:
0.0475
Gnomad ASJ
AF:
0.0173
Gnomad EAS
AF:
0.161
Gnomad SAS
AF:
0.0164
Gnomad FIN
AF:
0.00349
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.0202
Gnomad OTH
AF:
0.0703
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0825
AC:
12546
AN:
152068
Hom.:
1150
Cov.:
31
AF XY:
0.0805
AC XY:
5986
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.224
Gnomad4 AMR
AF:
0.0474
Gnomad4 ASJ
AF:
0.0173
Gnomad4 EAS
AF:
0.161
Gnomad4 SAS
AF:
0.0160
Gnomad4 FIN
AF:
0.00349
Gnomad4 NFE
AF:
0.0202
Gnomad4 OTH
AF:
0.0691
Alfa
AF:
0.0538
Hom.:
81
Bravo
AF:
0.0929
Asia WGS
AF:
0.106
AC:
368
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
6.7
Dann
Benign
0.72

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: rs10513430; hg19: chr3-152358401; API