GeneBe

6-80555778-C-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The variant allele was found at a frequency of 0.0000395 in 151,846 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000040 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

LOC648934
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.412

Publications

4 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC648934 n.80555778C>T intragenic_variant
LOC112267962XR_002956360.2 linkn.91-24535C>T intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000216352ENST00000403828.1 linkn.*63G>A downstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.0000395
AC:
6
AN:
151846
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000883
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
65818
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
37450
African (AFR)
AF:
0.00
AC:
0
AN:
1810
American (AMR)
AF:
0.00
AC:
0
AN:
7444
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
838
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3764
South Asian (SAS)
AF:
0.00
AC:
0
AN:
6100
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
14482
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
86
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
29054
Other (OTH)
AF:
0.00
AC:
0
AN:
2240
GnomAD4 genome
AF:
0.0000395
AC:
6
AN:
151846
Hom.:
0
Cov.:
31
AF XY:
0.0000270
AC XY:
2
AN XY:
74126
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
41324
American (AMR)
AF:
0.00
AC:
0
AN:
15242
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3468
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5170
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4816
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10546
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.0000883
AC:
6
AN:
67964
Other (OTH)
AF:
0.00
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.467
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
2449

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
7.6
DANN
Benign
0.90
PhyloP100
-0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs9449067; hg19: chr6-81265495; API