6-110977022-A-G

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 0.247 in 152,106 control chromosomes in the GnomAD database, including 5,387 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 0.25 ( 5387 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.342
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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:
0.248
AC:
37619
AN:
151988
Hom.:
5388
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.320
Gnomad AMI
AF:
0.247
Gnomad AMR
AF:
0.157
Gnomad ASJ
AF:
0.144
Gnomad EAS
AF:
0.652
Gnomad SAS
AF:
0.347
Gnomad FIN
AF:
0.296
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.185
Gnomad OTH
AF:
0.222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.247
AC:
37640
AN:
152106
Hom.:
5387
Cov.:
33
AF XY:
0.254
AC XY:
18911
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.320
Gnomad4 AMR
AF:
0.157
Gnomad4 ASJ
AF:
0.144
Gnomad4 EAS
AF:
0.652
Gnomad4 SAS
AF:
0.345
Gnomad4 FIN
AF:
0.296
Gnomad4 NFE
AF:
0.185
Gnomad4 OTH
AF:
0.227
Alfa
AF:
0.220
Hom.:
697
Bravo
AF:
0.234
Asia WGS
AF:
0.477
AC:
1660
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.6
DANN
Benign
0.65

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: rs9400442; hg19: chr6-111298225; API