17-43759255-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 0.614 in 151,968 control chromosomes in the GnomAD database, including 28,912 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 0.61 ( 28912 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.400
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=-0.71).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.637 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:
0.614
AC:
93193
AN:
151850
Hom.:
28877
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.582
Gnomad AMI
AF:
0.577
Gnomad AMR
AF:
0.562
Gnomad ASJ
AF:
0.622
Gnomad EAS
AF:
0.384
Gnomad SAS
AF:
0.655
Gnomad FIN
AF:
0.748
Gnomad MID
AF:
0.576
Gnomad NFE
AF:
0.640
Gnomad OTH
AF:
0.589
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.614
AC:
93275
AN:
151968
Hom.:
28912
Cov.:
32
AF XY:
0.617
AC XY:
45820
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.582
Gnomad4 AMR
AF:
0.561
Gnomad4 ASJ
AF:
0.622
Gnomad4 EAS
AF:
0.384
Gnomad4 SAS
AF:
0.656
Gnomad4 FIN
AF:
0.748
Gnomad4 NFE
AF:
0.639
Gnomad4 OTH
AF:
0.592
Alfa
AF:
0.550
Hom.:
2515
Bravo
AF:
0.593
Asia WGS
AF:
0.522
AC:
1817
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
5.9
DANN
Benign
0.90

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: rs851054; hg19: chr17-41836623; API