rs35967093

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 0.0792 in 151,918 control chromosomes in the GnomAD database, including 1,311 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 0.079 ( 1311 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.164
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=-0.61).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 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:
0.0792
AC:
12023
AN:
151800
Hom.:
1309
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.251
Gnomad AMI
AF:
0.0165
Gnomad AMR
AF:
0.0369
Gnomad ASJ
AF:
0.0199
Gnomad EAS
AF:
0.000387
Gnomad SAS
AF:
0.0114
Gnomad FIN
AF:
0.00104
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.0118
Gnomad OTH
AF:
0.0620
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0792
AC:
12038
AN:
151918
Hom.:
1311
Cov.:
31
AF XY:
0.0767
AC XY:
5697
AN XY:
74274
show subpopulations
Gnomad4 AFR
AF:
0.251
Gnomad4 AMR
AF:
0.0368
Gnomad4 ASJ
AF:
0.0199
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.0114
Gnomad4 FIN
AF:
0.00104
Gnomad4 NFE
AF:
0.0118
Gnomad4 OTH
AF:
0.0613
Alfa
AF:
0.0502
Hom.:
88
Bravo
AF:
0.0889
Asia WGS
AF:
0.0220
AC:
77
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
CADD
Benign
6.3
DANN
Benign
0.96

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: rs35967093; hg19: chr19-4883741; API