rs735718

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 0.0962 in 152,218 control chromosomes in the GnomAD database, including 943 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 0.096 ( 943 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.655
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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 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:
0.0963
AC:
14642
AN:
152100
Hom.:
943
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0270
Gnomad AMI
AF:
0.113
Gnomad AMR
AF:
0.117
Gnomad ASJ
AF:
0.145
Gnomad EAS
AF:
0.00116
Gnomad SAS
AF:
0.0711
Gnomad FIN
AF:
0.139
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.103
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0962
AC:
14646
AN:
152218
Hom.:
943
Cov.:
32
AF XY:
0.0948
AC XY:
7057
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0269
Gnomad4 AMR
AF:
0.118
Gnomad4 ASJ
AF:
0.145
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.0712
Gnomad4 FIN
AF:
0.139
Gnomad4 NFE
AF:
0.133
Gnomad4 OTH
AF:
0.102
Alfa
AF:
0.122
Hom.:
617
Bravo
AF:
0.0926
Asia WGS
AF:
0.0340
AC:
120
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
6.7
DANN
Benign
0.51

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: rs735718; hg19: chr3-70782197; API