rs10516308

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 0.412 in 151,850 control chromosomes in the GnomAD database, including 12,954 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 0.41 ( 12954 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.597
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=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.432 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:
0.412
AC:
62452
AN:
151732
Hom.:
12940
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.370
Gnomad AMI
AF:
0.629
Gnomad AMR
AF:
0.436
Gnomad ASJ
AF:
0.410
Gnomad EAS
AF:
0.272
Gnomad SAS
AF:
0.388
Gnomad FIN
AF:
0.447
Gnomad MID
AF:
0.358
Gnomad NFE
AF:
0.436
Gnomad OTH
AF:
0.390
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.412
AC:
62507
AN:
151850
Hom.:
12954
Cov.:
32
AF XY:
0.410
AC XY:
30457
AN XY:
74226
show subpopulations
Gnomad4 AFR
AF:
0.370
Gnomad4 AMR
AF:
0.437
Gnomad4 ASJ
AF:
0.410
Gnomad4 EAS
AF:
0.272
Gnomad4 SAS
AF:
0.390
Gnomad4 FIN
AF:
0.447
Gnomad4 NFE
AF:
0.436
Gnomad4 OTH
AF:
0.387
Alfa
AF:
0.443
Hom.:
1860
Bravo
AF:
0.411
Asia WGS
AF:
0.322
AC:
1120
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
3.5
DANN
Benign
0.47

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: rs10516308; hg19: chr4-17104182; API