rs1022298

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 0.478 in 152,042 control chromosomes in the GnomAD database, including 18,583 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 0.48 ( 18583 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0710
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=-0.74).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 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:
0.478
AC:
72655
AN:
151920
Hom.:
18559
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.622
Gnomad AMI
AF:
0.469
Gnomad AMR
AF:
0.385
Gnomad ASJ
AF:
0.423
Gnomad EAS
AF:
0.0195
Gnomad SAS
AF:
0.239
Gnomad FIN
AF:
0.471
Gnomad MID
AF:
0.427
Gnomad NFE
AF:
0.468
Gnomad OTH
AF:
0.483
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.478
AC:
72720
AN:
152042
Hom.:
18583
Cov.:
32
AF XY:
0.471
AC XY:
35030
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.622
Gnomad4 AMR
AF:
0.385
Gnomad4 ASJ
AF:
0.423
Gnomad4 EAS
AF:
0.0195
Gnomad4 SAS
AF:
0.241
Gnomad4 FIN
AF:
0.471
Gnomad4 NFE
AF:
0.468
Gnomad4 OTH
AF:
0.477
Alfa
AF:
0.457
Hom.:
33191
Bravo
AF:
0.477
Asia WGS
AF:
0.166
AC:
581
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
7.0
DANN
Benign
0.79

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: rs1022298; hg19: chr2-104142548; API