17-47691470-T-C

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 0.537 in 152,100 control chromosomes in the GnomAD database, including 22,457 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 0.54 ( 22457 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.469
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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:
0.537
AC:
81575
AN:
151980
Hom.:
22436
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.645
Gnomad AMI
AF:
0.512
Gnomad AMR
AF:
0.455
Gnomad ASJ
AF:
0.533
Gnomad EAS
AF:
0.447
Gnomad SAS
AF:
0.480
Gnomad FIN
AF:
0.468
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.513
Gnomad OTH
AF:
0.517
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.537
AC:
81635
AN:
152100
Hom.:
22457
Cov.:
32
AF XY:
0.532
AC XY:
39524
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.645
Gnomad4 AMR
AF:
0.454
Gnomad4 ASJ
AF:
0.533
Gnomad4 EAS
AF:
0.447
Gnomad4 SAS
AF:
0.481
Gnomad4 FIN
AF:
0.468
Gnomad4 NFE
AF:
0.512
Gnomad4 OTH
AF:
0.515
Alfa
AF:
0.506
Hom.:
25552
Bravo
AF:
0.540
Asia WGS
AF:
0.397
AC:
1383
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
4.0
DANN
Benign
0.75

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: rs8070463; hg19: chr17-45768836; API