rs1505863

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 0.252 in 152,034 control chromosomes in the GnomAD database, including 7,059 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 0.25 ( 7059 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.531
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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 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:
0.252
AC:
38218
AN:
151916
Hom.:
7049
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.477
Gnomad AMI
AF:
0.0811
Gnomad AMR
AF:
0.241
Gnomad ASJ
AF:
0.105
Gnomad EAS
AF:
0.607
Gnomad SAS
AF:
0.318
Gnomad FIN
AF:
0.103
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.119
Gnomad OTH
AF:
0.226
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.252
AC:
38268
AN:
152034
Hom.:
7059
Cov.:
32
AF XY:
0.253
AC XY:
18822
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.477
Gnomad4 AMR
AF:
0.242
Gnomad4 ASJ
AF:
0.105
Gnomad4 EAS
AF:
0.608
Gnomad4 SAS
AF:
0.318
Gnomad4 FIN
AF:
0.103
Gnomad4 NFE
AF:
0.119
Gnomad4 OTH
AF:
0.226
Alfa
AF:
0.206
Hom.:
734
Bravo
AF:
0.273
Asia WGS
AF:
0.417
AC:
1451
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
7.7
DANN
Benign
0.72

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: rs1505863; hg19: chr4-139611302; API