rs1575013

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 0.29 in 151,918 control chromosomes in the GnomAD database, including 7,923 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 0.29 ( 7923 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.338
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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 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:
0.290
AC:
43947
AN:
151798
Hom.:
7908
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.504
Gnomad AMI
AF:
0.213
Gnomad AMR
AF:
0.181
Gnomad ASJ
AF:
0.261
Gnomad EAS
AF:
0.0516
Gnomad SAS
AF:
0.370
Gnomad FIN
AF:
0.156
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.219
Gnomad OTH
AF:
0.289
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.290
AC:
43992
AN:
151918
Hom.:
7923
Cov.:
32
AF XY:
0.286
AC XY:
21231
AN XY:
74252
show subpopulations
Gnomad4 AFR
AF:
0.504
Gnomad4 AMR
AF:
0.181
Gnomad4 ASJ
AF:
0.261
Gnomad4 EAS
AF:
0.0520
Gnomad4 SAS
AF:
0.370
Gnomad4 FIN
AF:
0.156
Gnomad4 NFE
AF:
0.219
Gnomad4 OTH
AF:
0.285
Alfa
AF:
0.218
Hom.:
1788
Bravo
AF:
0.296
Asia WGS
AF:
0.207
AC:
720
AN:
3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.35
DANN
Benign
0.26

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: rs1575013; hg19: chr7-112728910; API