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GeneBe

rs6679677

chr1-113761186-C-Achr1-113761186-C-T

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 0.0656 in 152140 control chromosomes in the gnomAD Genomes 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

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd 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
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
2.4
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;