rs10506697

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 0.0749 in 152,264 control chromosomes in the GnomAD database, including 981 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 0.075 ( 981 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.124
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 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:
0.0750
AC:
11411
AN:
152146
Hom.:
978
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0754
Gnomad AMI
AF:
0.0154
Gnomad AMR
AF:
0.116
Gnomad ASJ
AF:
0.0429
Gnomad EAS
AF:
0.477
Gnomad SAS
AF:
0.138
Gnomad FIN
AF:
0.0515
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0370
Gnomad OTH
AF:
0.0688
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0749
AC:
11409
AN:
152264
Hom.:
981
Cov.:
32
AF XY:
0.0791
AC XY:
5889
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0752
Gnomad4 AMR
AF:
0.116
Gnomad4 ASJ
AF:
0.0429
Gnomad4 EAS
AF:
0.477
Gnomad4 SAS
AF:
0.136
Gnomad4 FIN
AF:
0.0515
Gnomad4 NFE
AF:
0.0370
Gnomad4 OTH
AF:
0.0719
Alfa
AF:
0.0672
Hom.:
95
Bravo
AF:
0.0817
Asia WGS
AF:
0.307
AC:
1067
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
6.4
DANN
Benign
0.73

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: rs10506697; hg19: chr12-74955474; API