6-167109907-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000705249.1(ENSG00000272980):​c.1066-26131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,996 control chromosomes in the GnomAD database, including 26,982 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 0.60 ( 26982 hom., cov: 32)

Consequence

ENSG00000272980
ENST00000705249.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.807
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.629 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
ENSG00000272980ENST00000705249.1 linkc.1066-26131A>G intron_variant Intron 11 of 12 ENSP00000516101.1 A0A994J5H4

Frequencies

GnomAD3 genomes
AF:
0.595
AC:
90400
AN:
151876
Hom.:
26934
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.574
Gnomad AMI
AF:
0.744
Gnomad AMR
AF:
0.639
Gnomad ASJ
AF:
0.612
Gnomad EAS
AF:
0.546
Gnomad SAS
AF:
0.610
Gnomad FIN
AF:
0.616
Gnomad MID
AF:
0.529
Gnomad NFE
AF:
0.595
Gnomad OTH
AF:
0.615
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.595
AC:
90510
AN:
151996
Hom.:
26982
Cov.:
32
AF XY:
0.596
AC XY:
44241
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.574
Gnomad4 AMR
AF:
0.640
Gnomad4 ASJ
AF:
0.612
Gnomad4 EAS
AF:
0.544
Gnomad4 SAS
AF:
0.611
Gnomad4 FIN
AF:
0.616
Gnomad4 NFE
AF:
0.595
Gnomad4 OTH
AF:
0.620
Alfa
AF:
0.595
Hom.:
21877
Bravo
AF:
0.598
Asia WGS
AF:
0.600
AC:
2082
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
1.3
DANN
Benign
0.39

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: rs6907666; hg19: chr6-167523395; API