GeneBe

6-160698207-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000448126.6(ENSG00000224477):​n.56C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,136 control chromosomes in the GnomAD database, including 6,328 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 0.26 ( 6327 hom., cov: 31)
Exomes 𝑓: 0.22 ( 1 hom. )

Consequence

ENSG00000224477
ENST00000448126.6 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0820

Publications

13 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 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
ENSG00000224477ENST00000448126.6 linkn.56C>T non_coding_transcript_exon_variant Exon 1 of 2 5

Frequencies

GnomAD3 genomes
AF:
0.263
AC:
40044
AN:
151986
Hom.:
6329
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.268
Gnomad AMR
AF:
0.410
Gnomad ASJ
AF:
0.261
Gnomad EAS
AF:
0.633
Gnomad SAS
AF:
0.364
Gnomad FIN
AF:
0.261
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.280
Gnomad OTH
AF:
0.275
GnomAD4 exome
AF:
0.219
AC:
7
AN:
32
Hom.:
1
AF XY:
0.192
AC XY:
5
AN XY:
26
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.233
AC:
7
AN:
30
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.535
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.263
AC:
40049
AN:
152104
Hom.:
6327
Cov.:
31
AF XY:
0.270
AC XY:
20103
AN XY:
74338
show subpopulations
African (AFR)
AF:
0.124
AC:
5162
AN:
41506
American (AMR)
AF:
0.410
AC:
6262
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.261
AC:
907
AN:
3470
East Asian (EAS)
AF:
0.633
AC:
3277
AN:
5174
South Asian (SAS)
AF:
0.364
AC:
1749
AN:
4810
European-Finnish (FIN)
AF:
0.261
AC:
2762
AN:
10566
Middle Eastern (MID)
AF:
0.184
AC:
54
AN:
294
European-Non Finnish (NFE)
AF:
0.280
AC:
19056
AN:
67978
Other (OTH)
AF:
0.272
AC:
576
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1455
2910
4366
5821
7276
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
410
820
1230
1640
2050
<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:
0.166
Hom.:
373
Bravo
AF:
0.270
Asia WGS
AF:
0.447
AC:
1553
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.5
DANN
Benign
0.82
PhyloP100
-0.082

Splicing

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

Publications

Other links and lift over

dbSNP: rs783144; hg19: chr6-161119239; COSMIC: COSV51981736; API