rs6679677

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 0.0655 in 152,258 control chromosomes in the GnomAD database, including 484 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 0.066 ( 484 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.276
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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0984 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:
0.0656
AC:
9974
AN:
152140
Hom.:
484
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0152
Gnomad AMI
AF:
0.0395
Gnomad AMR
AF:
0.0380
Gnomad ASJ
AF:
0.0501
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0122
Gnomad FIN
AF:
0.147
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.100
Gnomad OTH
AF:
0.0526
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0655
AC:
9974
AN:
152258
Hom.:
484
Cov.:
32
AF XY:
0.0644
AC XY:
4795
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0151
Gnomad4 AMR
AF:
0.0380
Gnomad4 ASJ
AF:
0.0501
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0124
Gnomad4 FIN
AF:
0.147
Gnomad4 NFE
AF:
0.100
Gnomad4 OTH
AF:
0.0516
Alfa
AF:
0.0853
Hom.:
941
Bravo
AF:
0.0555
Asia WGS
AF:
0.00866
AC:
31
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.5
DANN
Benign
0.66

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: rs6679677; hg19: chr1-114303808; API