rs10935268

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.177 in 151,838 control chromosomes in the GnomAD database, including 3,095 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 0.18 ( 3095 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.91
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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:
0.177
AC:
26901
AN:
151718
Hom.:
3084
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.331
Gnomad AMI
AF:
0.0890
Gnomad AMR
AF:
0.129
Gnomad ASJ
AF:
0.197
Gnomad EAS
AF:
0.0610
Gnomad SAS
AF:
0.0713
Gnomad FIN
AF:
0.0726
Gnomad MID
AF:
0.217
Gnomad NFE
AF:
0.127
Gnomad OTH
AF:
0.180
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.177
AC:
26940
AN:
151838
Hom.:
3095
Cov.:
32
AF XY:
0.171
AC XY:
12703
AN XY:
74204
show subpopulations
Gnomad4 AFR
AF:
0.331
Gnomad4 AMR
AF:
0.129
Gnomad4 ASJ
AF:
0.197
Gnomad4 EAS
AF:
0.0611
Gnomad4 SAS
AF:
0.0707
Gnomad4 FIN
AF:
0.0726
Gnomad4 NFE
AF:
0.127
Gnomad4 OTH
AF:
0.178
Alfa
AF:
0.134
Hom.:
3332
Bravo
AF:
0.188
Asia WGS
AF:
0.0890
AC:
310
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.26
CADD
Benign
17
DANN
Benign
0.74

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: rs10935268; hg19: chr3-137447485; API