rs1207739

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 0.0574 in 152,282 control chromosomes in the GnomAD database, including 328 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 0.057 ( 328 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.543
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=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0806 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0574
AC:
8738
AN:
152164
Hom.:
328
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0143
Gnomad AMI
AF:
0.160
Gnomad AMR
AF:
0.0526
Gnomad ASJ
AF:
0.0625
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0872
Gnomad FIN
AF:
0.107
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0776
Gnomad OTH
AF:
0.0584
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0574
AC:
8738
AN:
152282
Hom.:
328
Cov.:
33
AF XY:
0.0583
AC XY:
4342
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0142
Gnomad4 AMR
AF:
0.0525
Gnomad4 ASJ
AF:
0.0625
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0875
Gnomad4 FIN
AF:
0.107
Gnomad4 NFE
AF:
0.0776
Gnomad4 OTH
AF:
0.0578
Alfa
AF:
0.0711
Hom.:
634
Bravo
AF:
0.0507
Asia WGS
AF:
0.0330
AC:
116
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.87
DANN
Benign
0.60

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: rs1207739; hg19: chr7-96660192; API