rs6985069

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 0.672 in 152,022 control chromosomes in the GnomAD database, including 34,882 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 0.67 ( 34882 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.167
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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:
0.672
AC:
102055
AN:
151904
Hom.:
34870
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.559
Gnomad AMI
AF:
0.603
Gnomad AMR
AF:
0.608
Gnomad ASJ
AF:
0.800
Gnomad EAS
AF:
0.865
Gnomad SAS
AF:
0.770
Gnomad FIN
AF:
0.666
Gnomad MID
AF:
0.797
Gnomad NFE
AF:
0.727
Gnomad OTH
AF:
0.683
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.672
AC:
102111
AN:
152022
Hom.:
34882
Cov.:
32
AF XY:
0.670
AC XY:
49772
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.559
Gnomad4 AMR
AF:
0.608
Gnomad4 ASJ
AF:
0.800
Gnomad4 EAS
AF:
0.865
Gnomad4 SAS
AF:
0.770
Gnomad4 FIN
AF:
0.666
Gnomad4 NFE
AF:
0.727
Gnomad4 OTH
AF:
0.683
Alfa
AF:
0.674
Hom.:
5510
Bravo
AF:
0.663
Asia WGS
AF:
0.776
AC:
2698
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.6
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: rs6985069; hg19: chr8-28086088; API