GeneBe

22-46143761-C-T

Variant names:

Variant summary

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

The ENST00000846781.1(ENSG00000310052):​n.905C>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 0.356 in 152,154 control chromosomes in the GnomAD database, including 11,920 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 0.36 ( 11920 hom., cov: 33)

Consequence

ENSG00000310052
ENST00000846781.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.71

Publications

3 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 (Cadd=15.06).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846781.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt

There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ENSG00000310052
ENST00000846781.1
n.905C>T
non_coding_transcript_exon
Exon 3 of 3
ENSG00000310052
ENST00000846782.1
n.869C>T
non_coding_transcript_exon
Exon 3 of 3
ENSG00000310052
ENST00000846783.1
n.707C>T
non_coding_transcript_exon
Exon 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.356
AC:
54144
AN:
152036
Hom.:
11892
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.620
Gnomad AMI
AF:
0.421
Gnomad AMR
AF:
0.227
Gnomad ASJ
AF:
0.169
Gnomad EAS
AF:
0.0808
Gnomad SAS
AF:
0.201
Gnomad FIN
AF:
0.251
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.283
Gnomad OTH
AF:
0.327
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.356
AC:
54222
AN:
152154
Hom.:
11920
Cov.:
33
AF XY:
0.347
AC XY:
25852
AN XY:
74402
show subpopulations
African (AFR)
AF:
0.620
AC:
25715
AN:
41482
American (AMR)
AF:
0.227
AC:
3473
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
0.169
AC:
586
AN:
3472
East Asian (EAS)
AF:
0.0808
AC:
419
AN:
5188
South Asian (SAS)
AF:
0.202
AC:
975
AN:
4830
European-Finnish (FIN)
AF:
0.251
AC:
2659
AN:
10584
Middle Eastern (MID)
AF:
0.231
AC:
68
AN:
294
European-Non Finnish (NFE)
AF:
0.283
AC:
19263
AN:
67982
Other (OTH)
AF:
0.323
AC:
683
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1658
3315
4973
6630
8288
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
490
980
1470
1960
2450
<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:
0.380
Hom.:
5746
Bravo
AF:
0.367

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
CADD
Benign
15
PhyloP100
1.7

Splicing

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

Publications

Other links and lift over

dbSNP: rs135562; API