rs2011946

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 0.451 in 152,146 control chromosomes in the GnomAD database, including 19,655 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 0.45 ( 19655 hom., cov: 34)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.103
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.451
AC:
68582
AN:
152028
Hom.:
19649
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.200
Gnomad AMI
AF:
0.691
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.266
Gnomad EAS
AF:
0.115
Gnomad SAS
AF:
0.252
Gnomad FIN
AF:
0.644
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.656
Gnomad OTH
AF:
0.383
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.451
AC:
68611
AN:
152146
Hom.:
19655
Cov.:
34
AF XY:
0.441
AC XY:
32772
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.200
Gnomad4 AMR
AF:
0.305
Gnomad4 ASJ
AF:
0.266
Gnomad4 EAS
AF:
0.115
Gnomad4 SAS
AF:
0.253
Gnomad4 FIN
AF:
0.644
Gnomad4 NFE
AF:
0.656
Gnomad4 OTH
AF:
0.379
Alfa
AF:
0.562
Hom.:
16896
Bravo
AF:
0.418
Asia WGS
AF:
0.166
AC:
580
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.0
DANN
Benign
0.15

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: rs2011946; hg19: chr2-136817616; API