chr3-172497785-C-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 0.459 in 151,962 control chromosomes in the GnomAD database, including 16,299 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 0.46 ( 16299 hom., cov: 32)

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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 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:
0.459
AC:
69740
AN:
151844
Hom.:
16298
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.529
Gnomad AMI
AF:
0.486
Gnomad AMR
AF:
0.374
Gnomad ASJ
AF:
0.418
Gnomad EAS
AF:
0.483
Gnomad SAS
AF:
0.449
Gnomad FIN
AF:
0.442
Gnomad MID
AF:
0.363
Gnomad NFE
AF:
0.440
Gnomad OTH
AF:
0.457
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.459
AC:
69778
AN:
151962
Hom.:
16299
Cov.:
32
AF XY:
0.456
AC XY:
33860
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.529
Gnomad4 AMR
AF:
0.374
Gnomad4 ASJ
AF:
0.418
Gnomad4 EAS
AF:
0.482
Gnomad4 SAS
AF:
0.448
Gnomad4 FIN
AF:
0.442
Gnomad4 NFE
AF:
0.440
Gnomad4 OTH
AF:
0.455
Alfa
AF:
0.437
Hom.:
19997
Bravo
AF:
0.457
Asia WGS
AF:
0.515
AC:
1788
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
5.8
DANN
Benign
0.70

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: rs2041693; hg19: chr3-172215575; API