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GeneBe

rs903570

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 0.202 in 152,056 control chromosomes in the GnomAD database, including 5,833 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 0.20 ( 5833 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.154
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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 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:
0.202
AC:
30664
AN:
151938
Hom.:
5809
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.501
Gnomad AMI
AF:
0.0384
Gnomad AMR
AF:
0.115
Gnomad ASJ
AF:
0.115
Gnomad EAS
AF:
0.0209
Gnomad SAS
AF:
0.224
Gnomad FIN
AF:
0.0451
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.0831
Gnomad OTH
AF:
0.188
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.202
AC:
30726
AN:
152056
Hom.:
5833
Cov.:
31
AF XY:
0.198
AC XY:
14747
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.501
Gnomad4 AMR
AF:
0.115
Gnomad4 ASJ
AF:
0.115
Gnomad4 EAS
AF:
0.0207
Gnomad4 SAS
AF:
0.224
Gnomad4 FIN
AF:
0.0451
Gnomad4 NFE
AF:
0.0831
Gnomad4 OTH
AF:
0.187
Alfa
AF:
0.118
Hom.:
727
Bravo
AF:
0.216
Asia WGS
AF:
0.128
AC:
446
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
5.5
Dann
Benign
0.71

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: rs903570; hg19: chr12-49268519; COSMIC: COSV56451767; API