2-74785200-C-T

Variant summary

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

The ENST00000690069.2(ENSG00000286739):​n.534-20533C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,020 control chromosomes in the GnomAD database, including 38,268 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 0.70 ( 38268 hom., cov: 31)

Consequence

ENSG00000286739
ENST00000690069.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0620

Publications

6 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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 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
ENSG00000286739ENST00000690069.2 linkn.534-20533C>T intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.701
AC:
106521
AN:
151902
Hom.:
38230
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.851
Gnomad AMI
AF:
0.737
Gnomad AMR
AF:
0.669
Gnomad ASJ
AF:
0.669
Gnomad EAS
AF:
0.454
Gnomad SAS
AF:
0.579
Gnomad FIN
AF:
0.726
Gnomad MID
AF:
0.642
Gnomad NFE
AF:
0.643
Gnomad OTH
AF:
0.669
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.701
AC:
106600
AN:
152020
Hom.:
38268
Cov.:
31
AF XY:
0.701
AC XY:
52088
AN XY:
74320
show subpopulations
African (AFR)
AF:
0.851
AC:
35299
AN:
41490
American (AMR)
AF:
0.669
AC:
10212
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.669
AC:
2322
AN:
3470
East Asian (EAS)
AF:
0.454
AC:
2341
AN:
5162
South Asian (SAS)
AF:
0.580
AC:
2792
AN:
4814
European-Finnish (FIN)
AF:
0.726
AC:
7682
AN:
10574
Middle Eastern (MID)
AF:
0.636
AC:
187
AN:
294
European-Non Finnish (NFE)
AF:
0.643
AC:
43703
AN:
67934
Other (OTH)
AF:
0.661
AC:
1394
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1557
3114
4672
6229
7786
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
804
1608
2412
3216
4020
<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:
0.655
Hom.:
140385
Bravo
AF:
0.702
Asia WGS
AF:
0.496
AC:
1724
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.1
DANN
Benign
0.72
PhyloP100
-0.062

Splicing

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

Publications

Other links and lift over

dbSNP: rs6546923; hg19: chr2-75012327; API