10-56049270-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 0.0318 in 151,712 control chromosomes in the GnomAD database, including 93 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 0.032 ( 93 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.367
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=-0.96).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0683 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:
0.0318
AC:
4825
AN:
151594
Hom.:
93
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0167
Gnomad AMI
AF:
0.00441
Gnomad AMR
AF:
0.0365
Gnomad ASJ
AF:
0.0880
Gnomad EAS
AF:
0.0691
Gnomad SAS
AF:
0.0748
Gnomad FIN
AF:
0.0388
Gnomad MID
AF:
0.0769
Gnomad NFE
AF:
0.0299
Gnomad OTH
AF:
0.0437
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0318
AC:
4817
AN:
151712
Hom.:
93
Cov.:
32
AF XY:
0.0334
AC XY:
2479
AN XY:
74126
show subpopulations
Gnomad4 AFR
AF:
0.0166
Gnomad4 AMR
AF:
0.0363
Gnomad4 ASJ
AF:
0.0880
Gnomad4 EAS
AF:
0.0691
Gnomad4 SAS
AF:
0.0747
Gnomad4 FIN
AF:
0.0388
Gnomad4 NFE
AF:
0.0300
Gnomad4 OTH
AF:
0.0433
Alfa
AF:
0.0294
Hom.:
53
Bravo
AF:
0.0318
Asia WGS
AF:
0.0540
AC:
186
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.6
DANN
Benign
0.29

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: rs11005196; hg19: chr10-57809031; API