3-161786219-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.444 in 151,720 control chromosomes in the GnomAD database, including 15,648 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 0.44 ( 15648 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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:
0.444
AC:
67343
AN:
151604
Hom.:
15630
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.368
Gnomad AMI
AF:
0.197
Gnomad AMR
AF:
0.495
Gnomad ASJ
AF:
0.447
Gnomad EAS
AF:
0.845
Gnomad SAS
AF:
0.408
Gnomad FIN
AF:
0.524
Gnomad MID
AF:
0.481
Gnomad NFE
AF:
0.442
Gnomad OTH
AF:
0.428
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.444
AC:
67388
AN:
151720
Hom.:
15648
Cov.:
31
AF XY:
0.450
AC XY:
33401
AN XY:
74150
show subpopulations
Gnomad4 AFR
AF:
0.368
Gnomad4 AMR
AF:
0.496
Gnomad4 ASJ
AF:
0.447
Gnomad4 EAS
AF:
0.845
Gnomad4 SAS
AF:
0.408
Gnomad4 FIN
AF:
0.524
Gnomad4 NFE
AF:
0.442
Gnomad4 OTH
AF:
0.434
Alfa
AF:
0.447
Hom.:
27152
Bravo
AF:
0.447
Asia WGS
AF:
0.633
AC:
2197
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.33
CADD
Benign
17
DANN
Benign
0.67

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: rs1996264; hg19: chr3-161504007; API