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GeneBe

rs4444235

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 0.43 in 152,106 control chromosomes in the GnomAD database, including 14,506 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 0.43 ( 14506 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104
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=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 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:
0.431
AC:
65438
AN:
151988
Hom.:
14503
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.332
Gnomad AMI
AF:
0.461
Gnomad AMR
AF:
0.480
Gnomad ASJ
AF:
0.559
Gnomad EAS
AF:
0.490
Gnomad SAS
AF:
0.507
Gnomad FIN
AF:
0.417
Gnomad MID
AF:
0.570
Gnomad NFE
AF:
0.462
Gnomad OTH
AF:
0.477
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.430
AC:
65474
AN:
152106
Hom.:
14506
Cov.:
32
AF XY:
0.432
AC XY:
32152
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.332
Gnomad4 AMR
AF:
0.480
Gnomad4 ASJ
AF:
0.559
Gnomad4 EAS
AF:
0.491
Gnomad4 SAS
AF:
0.508
Gnomad4 FIN
AF:
0.417
Gnomad4 NFE
AF:
0.462
Gnomad4 OTH
AF:
0.481
Alfa
AF:
0.474
Hom.:
39490
Bravo
AF:
0.430
Asia WGS
AF:
0.491
AC:
1708
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
0.55
Dann
Benign
0.82

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: rs4444235; hg19: chr14-54410919; API