chr10-92705802-C-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 0.43 in 151,954 control chromosomes in the GnomAD database, including 14,670 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 0.43 ( 14670 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.429
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 (EAS) allele frequency at 95% confidence interval = 0.804 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:
0.430
AC:
65350
AN:
151838
Hom.:
14674
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.377
Gnomad AMI
AF:
0.538
Gnomad AMR
AF:
0.472
Gnomad ASJ
AF:
0.360
Gnomad EAS
AF:
0.825
Gnomad SAS
AF:
0.561
Gnomad FIN
AF:
0.477
Gnomad MID
AF:
0.335
Gnomad NFE
AF:
0.410
Gnomad OTH
AF:
0.423
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.430
AC:
65385
AN:
151954
Hom.:
14670
Cov.:
32
AF XY:
0.435
AC XY:
32328
AN XY:
74246
show subpopulations
Gnomad4 AFR
AF:
0.377
Gnomad4 AMR
AF:
0.472
Gnomad4 ASJ
AF:
0.360
Gnomad4 EAS
AF:
0.825
Gnomad4 SAS
AF:
0.560
Gnomad4 FIN
AF:
0.477
Gnomad4 NFE
AF:
0.410
Gnomad4 OTH
AF:
0.422
Alfa
AF:
0.422
Hom.:
30619
Bravo
AF:
0.430
Asia WGS
AF:
0.622
AC:
2158
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.45
DANN
Benign
0.77

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: rs5015480; hg19: chr10-94465559; API