4-140834736-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 0.805 in 152,156 control chromosomes in the GnomAD database, including 54,479 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 0.80 ( 54479 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.111
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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.973 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:
0.805
AC:
122435
AN:
152038
Hom.:
54469
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.387
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.908
Gnomad ASJ
AF:
0.945
Gnomad EAS
AF:
0.961
Gnomad SAS
AF:
0.918
Gnomad FIN
AF:
0.964
Gnomad MID
AF:
0.918
Gnomad NFE
AF:
0.980
Gnomad OTH
AF:
0.854
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.805
AC:
122485
AN:
152156
Hom.:
54479
Cov.:
32
AF XY:
0.809
AC XY:
60204
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.387
Gnomad4 AMR
AF:
0.908
Gnomad4 ASJ
AF:
0.945
Gnomad4 EAS
AF:
0.961
Gnomad4 SAS
AF:
0.919
Gnomad4 FIN
AF:
0.964
Gnomad4 NFE
AF:
0.980
Gnomad4 OTH
AF:
0.855
Alfa
AF:
0.928
Hom.:
24200
Bravo
AF:
0.782
Asia WGS
AF:
0.881
AC:
3059
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.9
DANN
Benign
0.32

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: rs1872861; hg19: chr4-141755890; API