3-32900360-G-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 0.623 in 151,978 control chromosomes in the GnomAD database, including 29,959 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 0.62 ( 29959 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 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:
0.623
AC:
94577
AN:
151860
Hom.:
29942
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.497
Gnomad AMI
AF:
0.550
Gnomad AMR
AF:
0.683
Gnomad ASJ
AF:
0.693
Gnomad EAS
AF:
0.761
Gnomad SAS
AF:
0.714
Gnomad FIN
AF:
0.642
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.663
Gnomad OTH
AF:
0.642
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.623
AC:
94638
AN:
151978
Hom.:
29959
Cov.:
31
AF XY:
0.625
AC XY:
46440
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.497
Gnomad4 AMR
AF:
0.684
Gnomad4 ASJ
AF:
0.693
Gnomad4 EAS
AF:
0.761
Gnomad4 SAS
AF:
0.713
Gnomad4 FIN
AF:
0.642
Gnomad4 NFE
AF:
0.663
Gnomad4 OTH
AF:
0.643
Alfa
AF:
0.642
Hom.:
12878
Bravo
AF:
0.621
Asia WGS
AF:
0.740
AC:
2574
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.16
DANN
Benign
0.84

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: rs7648704; hg19: chr3-32941852; API