rs1554690

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 0.423 in 151,782 control chromosomes in the GnomAD database, including 13,912 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 0.42 ( 13912 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.552
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 (AFR) allele frequency at 95% confidence interval = 0.5 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:
0.423
AC:
64172
AN:
151664
Hom.:
13882
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.505
Gnomad AMI
AF:
0.405
Gnomad AMR
AF:
0.295
Gnomad ASJ
AF:
0.405
Gnomad EAS
AF:
0.446
Gnomad SAS
AF:
0.482
Gnomad FIN
AF:
0.360
Gnomad MID
AF:
0.449
Gnomad NFE
AF:
0.407
Gnomad OTH
AF:
0.418
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.423
AC:
64244
AN:
151782
Hom.:
13912
Cov.:
32
AF XY:
0.420
AC XY:
31134
AN XY:
74170
show subpopulations
Gnomad4 AFR
AF:
0.506
Gnomad4 AMR
AF:
0.294
Gnomad4 ASJ
AF:
0.405
Gnomad4 EAS
AF:
0.446
Gnomad4 SAS
AF:
0.482
Gnomad4 FIN
AF:
0.360
Gnomad4 NFE
AF:
0.407
Gnomad4 OTH
AF:
0.417
Alfa
AF:
0.410
Hom.:
14585
Bravo
AF:
0.416
Asia WGS
AF:
0.471
AC:
1634
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.3
DANN
Benign
0.58

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: rs1554690; hg19: chr7-145746333; API