rs1361925

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 0.607 in 151,876 control chromosomes in the GnomAD database, including 28,269 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 0.61 ( 28269 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0980
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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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:
0.607
AC:
92101
AN:
151760
Hom.:
28252
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.646
Gnomad AMI
AF:
0.370
Gnomad AMR
AF:
0.623
Gnomad ASJ
AF:
0.649
Gnomad EAS
AF:
0.452
Gnomad SAS
AF:
0.428
Gnomad FIN
AF:
0.587
Gnomad MID
AF:
0.628
Gnomad NFE
AF:
0.607
Gnomad OTH
AF:
0.630
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.607
AC:
92156
AN:
151876
Hom.:
28269
Cov.:
31
AF XY:
0.603
AC XY:
44805
AN XY:
74248
show subpopulations
Gnomad4 AFR
AF:
0.646
Gnomad4 AMR
AF:
0.622
Gnomad4 ASJ
AF:
0.649
Gnomad4 EAS
AF:
0.453
Gnomad4 SAS
AF:
0.428
Gnomad4 FIN
AF:
0.587
Gnomad4 NFE
AF:
0.607
Gnomad4 OTH
AF:
0.623
Alfa
AF:
0.603
Hom.:
15113
Bravo
AF:
0.614
Asia WGS
AF:
0.422
AC:
1464
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
8.4
DANN
Benign
0.89

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: rs1361925; hg19: chr9-30085410; API