rs2882834

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 0.305 in 151,914 control chromosomes in the GnomAD database, including 7,730 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 0.30 ( 7730 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.450
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=-1.03).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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:
0.305
AC:
46259
AN:
151796
Hom.:
7723
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.198
Gnomad AMI
AF:
0.226
Gnomad AMR
AF:
0.355
Gnomad ASJ
AF:
0.330
Gnomad EAS
AF:
0.0530
Gnomad SAS
AF:
0.221
Gnomad FIN
AF:
0.348
Gnomad MID
AF:
0.329
Gnomad NFE
AF:
0.376
Gnomad OTH
AF:
0.319
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.305
AC:
46290
AN:
151914
Hom.:
7730
Cov.:
31
AF XY:
0.297
AC XY:
22046
AN XY:
74246
show subpopulations
Gnomad4 AFR
AF:
0.198
Gnomad4 AMR
AF:
0.355
Gnomad4 ASJ
AF:
0.330
Gnomad4 EAS
AF:
0.0531
Gnomad4 SAS
AF:
0.221
Gnomad4 FIN
AF:
0.348
Gnomad4 NFE
AF:
0.376
Gnomad4 OTH
AF:
0.320
Alfa
AF:
0.212
Hom.:
526
Bravo
AF:
0.300
Asia WGS
AF:
0.204
AC:
712
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.0
DANN
Benign
0.66

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: rs2882834; hg19: chr7-10364723; API