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GeneBe

rs1707420

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 0.558 in 151,942 control chromosomes in the GnomAD database, including 24,221 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 0.56 ( 24221 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76
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=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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:
0.558
AC:
84702
AN:
151824
Hom.:
24202
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.588
Gnomad AMI
AF:
0.471
Gnomad AMR
AF:
0.631
Gnomad ASJ
AF:
0.604
Gnomad EAS
AF:
0.889
Gnomad SAS
AF:
0.598
Gnomad FIN
AF:
0.479
Gnomad MID
AF:
0.585
Gnomad NFE
AF:
0.506
Gnomad OTH
AF:
0.557
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.558
AC:
84770
AN:
151942
Hom.:
24221
Cov.:
32
AF XY:
0.560
AC XY:
41587
AN XY:
74234
show subpopulations
Gnomad4 AFR
AF:
0.588
Gnomad4 AMR
AF:
0.632
Gnomad4 ASJ
AF:
0.604
Gnomad4 EAS
AF:
0.889
Gnomad4 SAS
AF:
0.599
Gnomad4 FIN
AF:
0.479
Gnomad4 NFE
AF:
0.506
Gnomad4 OTH
AF:
0.552
Alfa
AF:
0.526
Hom.:
37660
Bravo
AF:
0.570
Asia WGS
AF:
0.689
AC:
2394
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.27
Dann
Benign
0.43

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: rs1707420; hg19: chr8-5607663; API