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GeneBe

rs4444235

chr14-53944201-T-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 0.431 in 151988 control chromosomes in the gnomAD Genomes database, including 14503 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 ( 14503 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.491 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
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
1.8
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;