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GeneBe

rs4728142

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 0.377 in 152,036 control chromosomes in the GnomAD database, including 11,498 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 0.38 ( 11498 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.167
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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.377
AC:
57261
AN:
151920
Hom.:
11502
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.276
Gnomad AMI
AF:
0.458
Gnomad AMR
AF:
0.393
Gnomad ASJ
AF:
0.505
Gnomad EAS
AF:
0.122
Gnomad SAS
AF:
0.392
Gnomad FIN
AF:
0.396
Gnomad MID
AF:
0.481
Gnomad NFE
AF:
0.441
Gnomad OTH
AF:
0.411
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.377
AC:
57272
AN:
152036
Hom.:
11498
Cov.:
32
AF XY:
0.371
AC XY:
27601
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.275
Gnomad4 AMR
AF:
0.392
Gnomad4 ASJ
AF:
0.505
Gnomad4 EAS
AF:
0.122
Gnomad4 SAS
AF:
0.392
Gnomad4 FIN
AF:
0.396
Gnomad4 NFE
AF:
0.441
Gnomad4 OTH
AF:
0.408
Alfa
AF:
0.429
Hom.:
25053
Bravo
AF:
0.373
Asia WGS
AF:
0.241
AC:
840
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
1.9
Dann
Benign
0.41

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: rs4728142; hg19: chr7-128573967; API