rs7118561

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 0.3 in 152,142 control chromosomes in the GnomAD database, including 9,101 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 0.30 ( 9101 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0120
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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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:
0.300
AC:
45567
AN:
152024
Hom.:
9088
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.560
Gnomad AMI
AF:
0.0888
Gnomad AMR
AF:
0.209
Gnomad ASJ
AF:
0.214
Gnomad EAS
AF:
0.417
Gnomad SAS
AF:
0.370
Gnomad FIN
AF:
0.194
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.172
Gnomad OTH
AF:
0.279
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.300
AC:
45624
AN:
152142
Hom.:
9101
Cov.:
33
AF XY:
0.303
AC XY:
22569
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.560
Gnomad4 AMR
AF:
0.209
Gnomad4 ASJ
AF:
0.214
Gnomad4 EAS
AF:
0.417
Gnomad4 SAS
AF:
0.369
Gnomad4 FIN
AF:
0.194
Gnomad4 NFE
AF:
0.172
Gnomad4 OTH
AF:
0.277
Alfa
AF:
0.194
Hom.:
2660
Bravo
AF:
0.306
Asia WGS
AF:
0.408
AC:
1420
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
2.1
DANN
Benign
0.72

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: rs7118561; hg19: chr11-69058291; API