rs7583495

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 0.0828 in 150,738 control chromosomes in the GnomAD database, including 998 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 0.083 ( 998 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.89
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=-1.07).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0827
AC:
12458
AN:
150620
Hom.:
993
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.139
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.0543
Gnomad ASJ
AF:
0.0367
Gnomad EAS
AF:
0.0164
Gnomad SAS
AF:
0.0709
Gnomad FIN
AF:
0.0620
Gnomad MID
AF:
0.0701
Gnomad NFE
AF:
0.0689
Gnomad OTH
AF:
0.0528
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0828
AC:
12482
AN:
150738
Hom.:
998
Cov.:
31
AF XY:
0.0789
AC XY:
5810
AN XY:
73616
show subpopulations
Gnomad4 AFR
AF:
0.139
Gnomad4 AMR
AF:
0.0541
Gnomad4 ASJ
AF:
0.0367
Gnomad4 EAS
AF:
0.0163
Gnomad4 SAS
AF:
0.0703
Gnomad4 FIN
AF:
0.0620
Gnomad4 NFE
AF:
0.0689
Gnomad4 OTH
AF:
0.0523
Alfa
AF:
0.0780
Hom.:
96
Bravo
AF:
0.0838
Asia WGS
AF:
0.0430
AC:
148
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.017
DANN
Benign
0.68

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: rs7583495; hg19: chr2-90067598; API