4-4889421-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 0.563 in 152,110 control chromosomes in the GnomAD database, including 24,903 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 0.56 ( 24903 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.642
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 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:
0.563
AC:
85518
AN:
151992
Hom.:
24858
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.679
Gnomad AMI
AF:
0.291
Gnomad AMR
AF:
0.556
Gnomad ASJ
AF:
0.503
Gnomad EAS
AF:
0.784
Gnomad SAS
AF:
0.566
Gnomad FIN
AF:
0.635
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.473
Gnomad OTH
AF:
0.535
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.563
AC:
85617
AN:
152110
Hom.:
24903
Cov.:
33
AF XY:
0.572
AC XY:
42555
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.680
Gnomad4 AMR
AF:
0.556
Gnomad4 ASJ
AF:
0.503
Gnomad4 EAS
AF:
0.784
Gnomad4 SAS
AF:
0.566
Gnomad4 FIN
AF:
0.635
Gnomad4 NFE
AF:
0.473
Gnomad4 OTH
AF:
0.541
Alfa
AF:
0.489
Hom.:
31754
Bravo
AF:
0.559
Asia WGS
AF:
0.673
AC:
2342
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.95
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: rs6817411; hg19: chr4-4891148; API