rs7177055

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 0.583 in 152,030 control chromosomes in the GnomAD database, including 27,721 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 0.58 ( 27721 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0430
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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 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:
0.583
AC:
88621
AN:
151912
Hom.:
27695
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.725
Gnomad AMR
AF:
0.597
Gnomad ASJ
AF:
0.702
Gnomad EAS
AF:
0.354
Gnomad SAS
AF:
0.500
Gnomad FIN
AF:
0.675
Gnomad MID
AF:
0.680
Gnomad NFE
AF:
0.713
Gnomad OTH
AF:
0.603
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.583
AC:
88690
AN:
152030
Hom.:
27721
Cov.:
32
AF XY:
0.577
AC XY:
42853
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.366
Gnomad4 AMR
AF:
0.597
Gnomad4 ASJ
AF:
0.702
Gnomad4 EAS
AF:
0.355
Gnomad4 SAS
AF:
0.501
Gnomad4 FIN
AF:
0.675
Gnomad4 NFE
AF:
0.713
Gnomad4 OTH
AF:
0.602
Alfa
AF:
0.680
Hom.:
83564
Bravo
AF:
0.570
Asia WGS
AF:
0.466
AC:
1623
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.89
DANN
Benign
0.75

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: rs7177055; hg19: chr15-77832762; API