rs2870529

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 0.325 in 152,018 control chromosomes in the GnomAD database, including 9,036 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 0.32 ( 9036 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.106
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 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:
0.325
AC:
49336
AN:
151900
Hom.:
9037
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.173
Gnomad AMI
AF:
0.341
Gnomad AMR
AF:
0.396
Gnomad ASJ
AF:
0.309
Gnomad EAS
AF:
0.104
Gnomad SAS
AF:
0.207
Gnomad FIN
AF:
0.366
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.420
Gnomad OTH
AF:
0.344
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.325
AC:
49335
AN:
152018
Hom.:
9036
Cov.:
32
AF XY:
0.322
AC XY:
23924
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.173
Gnomad4 AMR
AF:
0.396
Gnomad4 ASJ
AF:
0.309
Gnomad4 EAS
AF:
0.104
Gnomad4 SAS
AF:
0.207
Gnomad4 FIN
AF:
0.366
Gnomad4 NFE
AF:
0.420
Gnomad4 OTH
AF:
0.340
Alfa
AF:
0.370
Hom.:
1364
Bravo
AF:
0.320
Asia WGS
AF:
0.145
AC:
505
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.4
DANN
Benign
0.20

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: rs2870529; hg19: chr19-29250570; API