10-90697125-G-T

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 0.212 in 152,118 control chromosomes in the GnomAD database, including 4,169 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 0.21 ( 4169 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.569
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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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:
0.212
AC:
32232
AN:
152000
Hom.:
4161
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.361
Gnomad AMI
AF:
0.109
Gnomad AMR
AF:
0.162
Gnomad ASJ
AF:
0.209
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.0636
Gnomad FIN
AF:
0.113
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.177
Gnomad OTH
AF:
0.202
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.212
AC:
32271
AN:
152118
Hom.:
4169
Cov.:
32
AF XY:
0.205
AC XY:
15282
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.361
Gnomad4 AMR
AF:
0.162
Gnomad4 ASJ
AF:
0.209
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.0637
Gnomad4 FIN
AF:
0.113
Gnomad4 NFE
AF:
0.177
Gnomad4 OTH
AF:
0.200
Alfa
AF:
0.175
Hom.:
1194
Bravo
AF:
0.222
Asia WGS
AF:
0.0600
AC:
207
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
2.1
DANN
Benign
0.54

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: rs11186275; hg19: chr10-92456882; API