6-110957720-G-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 0.14 in 142,376 control chromosomes in the GnomAD database, including 1,734 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 0.14 ( 1734 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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:
0.140
AC:
19876
AN:
142256
Hom.:
1727
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.253
Gnomad AMI
AF:
0.0637
Gnomad AMR
AF:
0.0889
Gnomad ASJ
AF:
0.141
Gnomad EAS
AF:
0.0514
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.0592
Gnomad MID
AF:
0.176
Gnomad NFE
AF:
0.0944
Gnomad OTH
AF:
0.136
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.140
AC:
19930
AN:
142376
Hom.:
1734
Cov.:
32
AF XY:
0.138
AC XY:
9566
AN XY:
69186
show subpopulations
Gnomad4 AFR
AF:
0.254
Gnomad4 AMR
AF:
0.0888
Gnomad4 ASJ
AF:
0.141
Gnomad4 EAS
AF:
0.0508
Gnomad4 SAS
AF:
0.152
Gnomad4 FIN
AF:
0.0592
Gnomad4 NFE
AF:
0.0944
Gnomad4 OTH
AF:
0.138
Alfa
AF:
0.0367
Hom.:
29
Bravo
AF:
0.174

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.89
DANN
Benign
0.17

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: rs9487562; hg19: chr6-111278923; API