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 rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein 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