chr6-95885976-A-C

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 0.657 in 151,970 control chromosomes in the GnomAD database, including 33,105 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 0.66 ( 33105 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.17
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=-1.04).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 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:
0.657
AC:
99791
AN:
151852
Hom.:
33071
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.662
Gnomad AMI
AF:
0.633
Gnomad AMR
AF:
0.544
Gnomad ASJ
AF:
0.660
Gnomad EAS
AF:
0.477
Gnomad SAS
AF:
0.693
Gnomad FIN
AF:
0.656
Gnomad MID
AF:
0.696
Gnomad NFE
AF:
0.691
Gnomad OTH
AF:
0.657
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.657
AC:
99871
AN:
151970
Hom.:
33105
Cov.:
31
AF XY:
0.650
AC XY:
48266
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.662
Gnomad4 AMR
AF:
0.544
Gnomad4 ASJ
AF:
0.660
Gnomad4 EAS
AF:
0.477
Gnomad4 SAS
AF:
0.694
Gnomad4 FIN
AF:
0.656
Gnomad4 NFE
AF:
0.691
Gnomad4 OTH
AF:
0.655
Alfa
AF:
0.657
Hom.:
5218
Bravo
AF:
0.647
Asia WGS
AF:
0.613
AC:
2134
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.1
DANN
Benign
0.56

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: rs2799652; hg19: chr6-96333852; API