rs2781551

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 0.789 in 152,018 control chromosomes in the GnomAD database, including 47,865 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 0.79 ( 47865 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.15
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.864 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:
0.789
AC:
119895
AN:
151900
Hom.:
47833
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.654
Gnomad AMI
AF:
0.780
Gnomad AMR
AF:
0.876
Gnomad ASJ
AF:
0.835
Gnomad EAS
AF:
0.786
Gnomad SAS
AF:
0.794
Gnomad FIN
AF:
0.914
Gnomad MID
AF:
0.827
Gnomad NFE
AF:
0.829
Gnomad OTH
AF:
0.828
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.789
AC:
119980
AN:
152018
Hom.:
47865
Cov.:
31
AF XY:
0.795
AC XY:
59095
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.655
Gnomad4 AMR
AF:
0.876
Gnomad4 ASJ
AF:
0.835
Gnomad4 EAS
AF:
0.786
Gnomad4 SAS
AF:
0.792
Gnomad4 FIN
AF:
0.914
Gnomad4 NFE
AF:
0.829
Gnomad4 OTH
AF:
0.831
Alfa
AF:
0.810
Hom.:
6241
Bravo
AF:
0.782
Asia WGS
AF:
0.775
AC:
2694
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.63
DANN
Benign
0.45

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: rs2781551; hg19: chr10-44862093; API