rs2577284

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 0.404 in 152,010 control chromosomes in the GnomAD database, including 15,726 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 0.40 ( 15726 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.208
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.403
AC:
61248
AN:
151892
Hom.:
15662
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.731
Gnomad AMI
AF:
0.402
Gnomad AMR
AF:
0.331
Gnomad ASJ
AF:
0.306
Gnomad EAS
AF:
0.471
Gnomad SAS
AF:
0.315
Gnomad FIN
AF:
0.285
Gnomad MID
AF:
0.315
Gnomad NFE
AF:
0.246
Gnomad OTH
AF:
0.367
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.404
AC:
61378
AN:
152010
Hom.:
15726
Cov.:
33
AF XY:
0.402
AC XY:
29883
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.732
Gnomad4 AMR
AF:
0.331
Gnomad4 ASJ
AF:
0.306
Gnomad4 EAS
AF:
0.471
Gnomad4 SAS
AF:
0.315
Gnomad4 FIN
AF:
0.285
Gnomad4 NFE
AF:
0.246
Gnomad4 OTH
AF:
0.375
Alfa
AF:
0.286
Hom.:
7792
Bravo
AF:
0.423
Asia WGS
AF:
0.462
AC:
1606
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.46
DANN
Benign
0.73

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: rs2577284; hg19: chr2-224929412; API