rs1703940

Positions:

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 0.892 in 152,026 control chromosomes in the GnomAD database, including 60,822 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 0.89 ( 60822 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.142
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.892
AC:
135442
AN:
151908
Hom.:
60753
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.977
Gnomad AMI
AF:
0.940
Gnomad AMR
AF:
0.922
Gnomad ASJ
AF:
0.900
Gnomad EAS
AF:
0.817
Gnomad SAS
AF:
0.915
Gnomad FIN
AF:
0.715
Gnomad MID
AF:
0.886
Gnomad NFE
AF:
0.863
Gnomad OTH
AF:
0.898
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.892
AC:
135570
AN:
152026
Hom.:
60822
Cov.:
30
AF XY:
0.885
AC XY:
65738
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.977
Gnomad4 AMR
AF:
0.922
Gnomad4 ASJ
AF:
0.900
Gnomad4 EAS
AF:
0.818
Gnomad4 SAS
AF:
0.915
Gnomad4 FIN
AF:
0.715
Gnomad4 NFE
AF:
0.863
Gnomad4 OTH
AF:
0.899
Alfa
AF:
0.876
Hom.:
76708
Bravo
AF:
0.910
Asia WGS
AF:
0.901
AC:
3108
AN:
3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.4
DANN
Benign
0.68

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: rs1703940; hg19: chr8-504401; API