4-141520513-G-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 0.268 in 152,144 control chromosomes in the GnomAD database, including 6,710 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 0.27 ( 6710 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.484
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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 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:
0.268
AC:
40744
AN:
152026
Hom.:
6680
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.459
Gnomad AMI
AF:
0.106
Gnomad AMR
AF:
0.296
Gnomad ASJ
AF:
0.188
Gnomad EAS
AF:
0.216
Gnomad SAS
AF:
0.190
Gnomad FIN
AF:
0.127
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.183
Gnomad OTH
AF:
0.262
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.268
AC:
40840
AN:
152144
Hom.:
6710
Cov.:
33
AF XY:
0.265
AC XY:
19741
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.460
Gnomad4 AMR
AF:
0.296
Gnomad4 ASJ
AF:
0.188
Gnomad4 EAS
AF:
0.215
Gnomad4 SAS
AF:
0.191
Gnomad4 FIN
AF:
0.127
Gnomad4 NFE
AF:
0.183
Gnomad4 OTH
AF:
0.262
Alfa
AF:
0.0972
Hom.:
134
Bravo
AF:
0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.77
DANN
Benign
0.45

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: rs1402812; hg19: chr4-142441666; API