5-170739590-A-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 0.166 in 152,118 control chromosomes in the GnomAD database, including 3,930 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 0.17 ( 3930 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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:
0.166
AC:
25278
AN:
152000
Hom.:
3925
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0479
Gnomad AMI
AF:
0.137
Gnomad AMR
AF:
0.320
Gnomad ASJ
AF:
0.100
Gnomad EAS
AF:
0.811
Gnomad SAS
AF:
0.359
Gnomad FIN
AF:
0.158
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.147
Gnomad OTH
AF:
0.155
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.166
AC:
25292
AN:
152118
Hom.:
3930
Cov.:
32
AF XY:
0.177
AC XY:
13191
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.0478
Gnomad4 AMR
AF:
0.321
Gnomad4 ASJ
AF:
0.100
Gnomad4 EAS
AF:
0.811
Gnomad4 SAS
AF:
0.359
Gnomad4 FIN
AF:
0.158
Gnomad4 NFE
AF:
0.147
Gnomad4 OTH
AF:
0.157
Alfa
AF:
0.0774
Hom.:
106
Bravo
AF:
0.175
Asia WGS
AF:
0.519
AC:
1802
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.97
DANN
Benign
0.56

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: rs17673653; hg19: chr5-170166594; API