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GeneBe

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/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE 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