rs35721

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 0.437 in 151,970 control chromosomes in the GnomAD database, including 16,642 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 0.44 ( 16642 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.116
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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 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:
0.437
AC:
66341
AN:
151854
Hom.:
16639
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.204
Gnomad AMI
AF:
0.550
Gnomad AMR
AF:
0.386
Gnomad ASJ
AF:
0.533
Gnomad EAS
AF:
0.218
Gnomad SAS
AF:
0.466
Gnomad FIN
AF:
0.502
Gnomad MID
AF:
0.535
Gnomad NFE
AF:
0.587
Gnomad OTH
AF:
0.458
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.437
AC:
66353
AN:
151970
Hom.:
16642
Cov.:
32
AF XY:
0.431
AC XY:
32033
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.204
Gnomad4 AMR
AF:
0.385
Gnomad4 ASJ
AF:
0.533
Gnomad4 EAS
AF:
0.219
Gnomad4 SAS
AF:
0.467
Gnomad4 FIN
AF:
0.502
Gnomad4 NFE
AF:
0.587
Gnomad4 OTH
AF:
0.459
Alfa
AF:
0.501
Hom.:
2560
Bravo
AF:
0.417
Asia WGS
AF:
0.324
AC:
1131
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
7.6
DANN
Benign
0.82

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: rs35721; hg19: chr12-100964371; API