rs2207081

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 0.361 in 111,421 control chromosomes in the GnomAD database, including 9,234 homozygotes. There are 11,350 hemizygotes in GnomAD. 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 0.36 ( 9234 hom., 11350 hem., cov: 23)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.544
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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:
0.360
AC:
40148
AN:
111369
Hom.:
9224
Cov.:
23
AF XY:
0.337
AC XY:
11300
AN XY:
33581
show subpopulations
Gnomad AFR
AF:
0.864
Gnomad AMI
AF:
0.118
Gnomad AMR
AF:
0.177
Gnomad ASJ
AF:
0.104
Gnomad EAS
AF:
0.00168
Gnomad SAS
AF:
0.0819
Gnomad FIN
AF:
0.176
Gnomad MID
AF:
0.248
Gnomad NFE
AF:
0.185
Gnomad OTH
AF:
0.315
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.361
AC:
40212
AN:
111421
Hom.:
9234
Cov.:
23
AF XY:
0.337
AC XY:
11350
AN XY:
33643
show subpopulations
Gnomad4 AFR
AF:
0.865
Gnomad4 AMR
AF:
0.176
Gnomad4 ASJ
AF:
0.104
Gnomad4 EAS
AF:
0.00169
Gnomad4 SAS
AF:
0.0818
Gnomad4 FIN
AF:
0.176
Gnomad4 NFE
AF:
0.185
Gnomad4 OTH
AF:
0.312
Alfa
AF:
0.235
Hom.:
2320
Bravo
AF:
0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.17
DANN
Benign
0.54

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: rs2207081; hg19: chrX-66573698; API