rs2886920

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 0.333 in 152,040 control chromosomes in the GnomAD database, including 9,257 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 0.33 ( 9257 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75
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=-1.06).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 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:
0.333
AC:
50583
AN:
151922
Hom.:
9263
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.415
Gnomad AMR
AF:
0.315
Gnomad ASJ
AF:
0.361
Gnomad EAS
AF:
0.391
Gnomad SAS
AF:
0.332
Gnomad FIN
AF:
0.374
Gnomad MID
AF:
0.294
Gnomad NFE
AF:
0.421
Gnomad OTH
AF:
0.347
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.333
AC:
50588
AN:
152040
Hom.:
9257
Cov.:
32
AF XY:
0.329
AC XY:
24412
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.173
Gnomad4 AMR
AF:
0.314
Gnomad4 ASJ
AF:
0.361
Gnomad4 EAS
AF:
0.389
Gnomad4 SAS
AF:
0.332
Gnomad4 FIN
AF:
0.374
Gnomad4 NFE
AF:
0.421
Gnomad4 OTH
AF:
0.345
Alfa
AF:
0.396
Hom.:
11949
Bravo
AF:
0.324
Asia WGS
AF:
0.320
AC:
1112
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.28
DANN
Benign
0.39

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: rs2886920; hg19: chr4-74626945; API