rs1953358

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 0.466 in 152,044 control chromosomes in the GnomAD database, including 16,904 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 0.47 ( 16904 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.389
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=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 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:
0.466
AC:
70812
AN:
151926
Hom.:
16886
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.400
Gnomad AMI
AF:
0.628
Gnomad AMR
AF:
0.484
Gnomad ASJ
AF:
0.537
Gnomad EAS
AF:
0.663
Gnomad SAS
AF:
0.497
Gnomad FIN
AF:
0.421
Gnomad MID
AF:
0.506
Gnomad NFE
AF:
0.486
Gnomad OTH
AF:
0.458
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.466
AC:
70861
AN:
152044
Hom.:
16904
Cov.:
33
AF XY:
0.465
AC XY:
34545
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.400
Gnomad4 AMR
AF:
0.485
Gnomad4 ASJ
AF:
0.537
Gnomad4 EAS
AF:
0.662
Gnomad4 SAS
AF:
0.496
Gnomad4 FIN
AF:
0.421
Gnomad4 NFE
AF:
0.486
Gnomad4 OTH
AF:
0.458
Alfa
AF:
0.492
Hom.:
34740
Bravo
AF:
0.472
Asia WGS
AF:
0.537
AC:
1867
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.28
DANN
Benign
0.60

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: rs1953358; hg19: chr14-56295580; API