6-11811081-C-T

Variant summary

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

The ENST00000412132.2(ENSG00000234427):​n.823C>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 0.508 in 152,144 control chromosomes in the GnomAD database, including 22,539 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 0.51 ( 22537 hom., cov: 32)
Exomes 𝑓: 0.37 ( 2 hom. )

Consequence

ENSG00000234427
ENST00000412132.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0890

Publications

9 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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC107986567XR_001743970.2 linkn.186G>A non_coding_transcript_exon_variant Exon 1 of 3
LOC124901257XR_007059451.1 linkn.*18C>T downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000234427ENST00000412132.2 linkn.823C>T non_coding_transcript_exon_variant Exon 2 of 2 3
ENSG00000234427ENST00000761720.1 linkn.700C>T non_coding_transcript_exon_variant Exon 2 of 2
ENSG00000234427ENST00000761721.1 linkn.333C>T non_coding_transcript_exon_variant Exon 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.507
AC:
77098
AN:
151980
Hom.:
22488
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.807
Gnomad AMI
AF:
0.322
Gnomad AMR
AF:
0.487
Gnomad ASJ
AF:
0.429
Gnomad EAS
AF:
0.498
Gnomad SAS
AF:
0.545
Gnomad FIN
AF:
0.454
Gnomad MID
AF:
0.386
Gnomad NFE
AF:
0.343
Gnomad OTH
AF:
0.478
GnomAD4 exome
AF:
0.370
AC:
17
AN:
46
Hom.:
2
Cov.:
0
AF XY:
0.467
AC XY:
14
AN XY:
30
show subpopulations
African (AFR)
AF:
0.500
AC:
1
AN:
2
American (AMR)
AF:
0.500
AC:
1
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
1.00
AC:
2
AN:
2
South Asian (SAS)
AF:
1.00
AC:
2
AN:
2
European-Finnish (FIN)
AF:
0.500
AC:
2
AN:
4
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.281
AC:
9
AN:
32
Other (OTH)
AF:
0.00
AC:
0
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.560
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:
0.508
AC:
77204
AN:
152098
Hom.:
22537
Cov.:
32
AF XY:
0.513
AC XY:
38135
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.808
AC:
33516
AN:
41504
American (AMR)
AF:
0.487
AC:
7447
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.429
AC:
1488
AN:
3468
East Asian (EAS)
AF:
0.497
AC:
2567
AN:
5162
South Asian (SAS)
AF:
0.544
AC:
2622
AN:
4818
European-Finnish (FIN)
AF:
0.454
AC:
4804
AN:
10570
Middle Eastern (MID)
AF:
0.398
AC:
117
AN:
294
European-Non Finnish (NFE)
AF:
0.343
AC:
23331
AN:
67976
Other (OTH)
AF:
0.482
AC:
1018
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1671
3342
5014
6685
8356
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
642
1284
1926
2568
3210
<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:
0.399
Hom.:
9226
Bravo
AF:
0.521
Asia WGS
AF:
0.553
AC:
1927
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.6
DANN
Benign
0.35
PhyloP100
0.089

Splicing

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

Publications

Other links and lift over

dbSNP: rs3950186; hg19: chr6-11811314; API