chr17-47754581-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 0.102 in 152,180 control chromosomes in the GnomAD database, including 855 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 0.10 ( 855 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.119
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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 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:
0.102
AC:
15549
AN:
152062
Hom.:
852
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.0482
Gnomad AMR
AF:
0.111
Gnomad ASJ
AF:
0.0953
Gnomad EAS
AF:
0.0606
Gnomad SAS
AF:
0.209
Gnomad FIN
AF:
0.0740
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0890
Gnomad OTH
AF:
0.0941
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.102
AC:
15564
AN:
152180
Hom.:
855
Cov.:
31
AF XY:
0.104
AC XY:
7752
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.123
Gnomad4 AMR
AF:
0.111
Gnomad4 ASJ
AF:
0.0953
Gnomad4 EAS
AF:
0.0604
Gnomad4 SAS
AF:
0.209
Gnomad4 FIN
AF:
0.0740
Gnomad4 NFE
AF:
0.0891
Gnomad4 OTH
AF:
0.0936
Alfa
AF:
0.0939
Hom.:
151
Bravo
AF:
0.103
Asia WGS
AF:
0.146
AC:
511
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
5.3
DANN
Benign
0.80

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: rs41515744; hg19: chr17-45831947; API