3-106314580-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 0.423 in 152,078 control chromosomes in the GnomAD database, including 13,823 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 0.42 ( 13823 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.184
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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.515 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:
0.423
AC:
64211
AN:
151960
Hom.:
13796
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.339
Gnomad AMI
AF:
0.397
Gnomad AMR
AF:
0.482
Gnomad ASJ
AF:
0.376
Gnomad EAS
AF:
0.361
Gnomad SAS
AF:
0.531
Gnomad FIN
AF:
0.472
Gnomad MID
AF:
0.434
Gnomad NFE
AF:
0.452
Gnomad OTH
AF:
0.427
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.423
AC:
64263
AN:
152078
Hom.:
13823
Cov.:
33
AF XY:
0.428
AC XY:
31789
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.338
Gnomad4 AMR
AF:
0.482
Gnomad4 ASJ
AF:
0.376
Gnomad4 EAS
AF:
0.361
Gnomad4 SAS
AF:
0.532
Gnomad4 FIN
AF:
0.472
Gnomad4 NFE
AF:
0.452
Gnomad4 OTH
AF:
0.433
Alfa
AF:
0.450
Hom.:
7873
Bravo
AF:
0.416
Asia WGS
AF:
0.472
AC:
1642
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
7.6
DANN
Benign
0.46

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: rs9873496; hg19: chr3-106033427; API