rs10134770

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 0.188 in 152,198 control chromosomes in the GnomAD database, including 3,179 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 0.19 ( 3179 hom., cov: 33)
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48
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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.188
AC:
28588
AN:
152080
Hom.:
3181
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0783
Gnomad AMI
AF:
0.218
Gnomad AMR
AF:
0.146
Gnomad ASJ
AF:
0.218
Gnomad EAS
AF:
0.214
Gnomad SAS
AF:
0.200
Gnomad FIN
AF:
0.262
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.248
Gnomad OTH
AF:
0.197
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.188
AC:
28585
AN:
152198
Hom.:
3179
Cov.:
33
AF XY:
0.188
AC XY:
13993
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.0782
Gnomad4 AMR
AF:
0.146
Gnomad4 ASJ
AF:
0.218
Gnomad4 EAS
AF:
0.214
Gnomad4 SAS
AF:
0.200
Gnomad4 FIN
AF:
0.262
Gnomad4 NFE
AF:
0.247
Gnomad4 OTH
AF:
0.195
Alfa
AF:
0.224
Hom.:
1942
Bravo
AF:
0.174
Asia WGS
AF:
0.181
AC:
630
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.82
DANN
Benign
0.41

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: rs10134770; hg19: chr14-65063315; API