4-145983152-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 0.365 in 149,064 control chromosomes in the GnomAD database, including 10,567 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 0.37 ( 10567 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490
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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 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:
0.366
AC:
54448
AN:
148946
Hom.:
10567
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.341
Gnomad AMI
AF:
0.444
Gnomad AMR
AF:
0.354
Gnomad ASJ
AF:
0.257
Gnomad EAS
AF:
0.0877
Gnomad SAS
AF:
0.378
Gnomad FIN
AF:
0.324
Gnomad MID
AF:
0.339
Gnomad NFE
AF:
0.415
Gnomad OTH
AF:
0.318
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.365
AC:
54478
AN:
149064
Hom.:
10567
Cov.:
32
AF XY:
0.356
AC XY:
25960
AN XY:
72852
show subpopulations
Gnomad4 AFR
AF:
0.341
Gnomad4 AMR
AF:
0.354
Gnomad4 ASJ
AF:
0.257
Gnomad4 EAS
AF:
0.0875
Gnomad4 SAS
AF:
0.377
Gnomad4 FIN
AF:
0.324
Gnomad4 NFE
AF:
0.415
Gnomad4 OTH
AF:
0.317
Alfa
AF:
0.398
Hom.:
20804
Bravo
AF:
0.356
Asia WGS
AF:
0.248
AC:
859
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
6.7
DANN
Benign
0.73

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: rs11100904; hg19: chr4-146904304; API