rs1544459

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 0.544 in 151,968 control chromosomes in the GnomAD database, including 24,556 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 0.54 ( 24556 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.259
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 (AFR) allele frequency at 95% confidence interval = 0.79 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:
0.544
AC:
82575
AN:
151850
Hom.:
24500
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.797
Gnomad AMI
AF:
0.585
Gnomad AMR
AF:
0.464
Gnomad ASJ
AF:
0.553
Gnomad EAS
AF:
0.319
Gnomad SAS
AF:
0.543
Gnomad FIN
AF:
0.368
Gnomad MID
AF:
0.475
Gnomad NFE
AF:
0.452
Gnomad OTH
AF:
0.529
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.544
AC:
82697
AN:
151968
Hom.:
24556
Cov.:
31
AF XY:
0.538
AC XY:
39959
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.797
Gnomad4 AMR
AF:
0.463
Gnomad4 ASJ
AF:
0.553
Gnomad4 EAS
AF:
0.320
Gnomad4 SAS
AF:
0.543
Gnomad4 FIN
AF:
0.368
Gnomad4 NFE
AF:
0.452
Gnomad4 OTH
AF:
0.532
Alfa
AF:
0.504
Hom.:
3343
Bravo
AF:
0.557
Asia WGS
AF:
0.528
AC:
1837
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
0.90
DANN
Benign
0.20

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: rs1544459; hg19: chr7-77417584; API