rs2070898

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 0.233 in 152,132 control chromosomes in the GnomAD database, including 5,586 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 0.23 ( 5586 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.387
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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:
0.234
AC:
35509
AN:
152014
Hom.:
5595
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0959
Gnomad AMI
AF:
0.333
Gnomad AMR
AF:
0.187
Gnomad ASJ
AF:
0.237
Gnomad EAS
AF:
0.800
Gnomad SAS
AF:
0.482
Gnomad FIN
AF:
0.201
Gnomad MID
AF:
0.252
Gnomad NFE
AF:
0.271
Gnomad OTH
AF:
0.240
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.233
AC:
35490
AN:
152132
Hom.:
5586
Cov.:
32
AF XY:
0.237
AC XY:
17632
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.0958
Gnomad4 AMR
AF:
0.186
Gnomad4 ASJ
AF:
0.237
Gnomad4 EAS
AF:
0.800
Gnomad4 SAS
AF:
0.480
Gnomad4 FIN
AF:
0.201
Gnomad4 NFE
AF:
0.271
Gnomad4 OTH
AF:
0.239
Alfa
AF:
0.250
Hom.:
648
Bravo
AF:
0.223
Asia WGS
AF:
0.474
AC:
1644
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.65
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: rs2070898; hg19: chr4-100243297; API